scientific-computing-system 2.2.7__tar.gz → 2.2.8__tar.gz

{scientific_computing_system-2.2.7 → scientific_computing_system-2.2.8}/CHANGELOG.md

@@ -1,1775 +1,1795 @@
-# Changelog
-
-All notable changes to **scientific-computing-system** will be documented in this file.
-
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
-and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-
-## [v2.2.6] - 2026-10-13
-
-### Housekeeping — second-round neighbour sweep
-
-- `transpose` shares the ragged-input contract the rest of the matrix API has
-  held since 2.2.5. It indexed only the leading row's width, so a short row
-  lost entries silently (`[[1.0],[2.0,3.0]]` became `[[1.0, 2.0]]`): the
-  result described a matrix nobody supplied. It now fails closed through the
-  same `_require_rectangular` check `mat_mul` and Cholesky use.
-- Geometric PMF boundary pinned: `geometric_pmf(0, p)` is 0 (no trial counted
-  1-based), and extreme `(k, p)` stays finite.
-- `poisson_pmf(0, 0)` is 1 and the log-space PMFs were probed at their
-  previously-crashing inputs; no remaining overflow class found in the
-  probability module.
-
-## [v2.2.5] - 2026-10-12
-
-### Housekeeping — audit hardening
-
-- Closes the findings of the full-repository audit: patched the concrete
-  defects (correctness, fail-closed behaviour, platform independence),
-  wired every standalone guard into CI, removed dead or duplicated code
-  paths, and pinned every doc claim to a test so it cannot silently
-  drift again. Regression tests fail without the corresponding fix.
-
-## [Unreleased]
-
-### Distribution status of 2.2.2 — read this before assuming npm has it
-
-The two registries are **not** in the same state for 2.2.2.
-
-| Registry | `2.2.2` | Build attestation |
-|---|---|---|
-| **PyPI** `scientific-computing-system` | **published** | **PEP 740 provenance present** |
-| **npm** `scientific-computing-system` | **NOT published** | none — the version does not exist on npm |
-
-PyPI 2.2.2 is live and carries a PEP 740 attestation. Verified against the live
-registries on 2026-10-05: the PEP 740 per-file provenance endpoint returns
-**HTTP 200** for both files.
-
-```
-curl -sS -o /dev/null -w '%{http_code}\n' \
-  https://pypi.org/integrity/scientific-computing-system/2.2.2/scientific_computing_system-2.2.2-py3-none-any.whl/provenance   # 200
-curl -sS -o /dev/null -w '%{http_code}\n' \
-  https://pypi.org/integrity/scientific-computing-system/2.2.2/scientific_computing_system-2.2.2.tar.gz/provenance               # 200
-```
-
-npm 2.2.2 does not exist. The published npm versions remain `1.0.0`, `2.2.0` and
-`2.2.1`. Nothing about the npm launcher is broken — the publish is blocked on a
-one-time npmjs.com registration, described next.
-
-### Pending: register the npm trusted publisher (one-time, maintainer, in a browser)
-
-npmjs.com has **no trusted publisher** configured for the package
-`scientific-computing-system`. Until one exists, the OIDC path cannot complete a
-publish, and npm publishes no provenance for this package.
-
-The coordinates to enter on npmjs.com → package `scientific-computing-system` →
-**Settings → Trusted Publisher → GitHub Actions**:
-
-| Field | Value |
-|---|---|
-| Organization or user | `Furox-Art` |
-| Package | `scientific-computing-system` |
-| Workflow filename | `npm-publish.yml` |
-| Environment name | `npm` |
-| Allowed actions | **`npm publish`** — must be enabled, see the warning below |
-
-**The allowed-actions field is not optional in practice.** npm's current UI grants
-`npm stage publish` by default on newly created configurations and makes direct
-`npm publish` **opt-in**. This repository's workflow calls `npm publish` directly,
-so registering the publisher *without* also allowing `npm publish` will leave the
-publish failing — with a permission error this time rather than a 404.
-
-The same registration from the CLI, using the maintainer's own npm login and 2FA:
-
-```
-npm trust github --file npm-publish.yml \
-  --repo Furox-Art/scientific-computing-system --env npm --allow-publish
-```
-
-### The publish mode default is unchanged, and was never set to token
-
-The mode is the `workflow_dispatch` input `use_token_fallback`, whose default is
-`false` — that is **OIDC**. There is no `npm_publish_mode` variable; the repository
-has **no Actions variables at all** (none at repository or organization scope), and
-`npm_publish_mode` appears nowhere in the tree. Nothing needs to be switched back:
-OIDC is already the default, and token mode remains an explicit per-run opt-in.
-
-`NPM_TOKEN` does still exist as a repository secret. It is what token mode would
-use, and it should be deleted once the trusted publisher is registered and the
-first OIDC publish has succeeded.
-
-### Fixed: a 404 from npm no longer reads as "already published"
-
-`npm publish` answered
-
-```
-npm error 404 The requested resource 'scientific-computing-system@2.2.2' could not
-be found or you do not have permission to access it.
-```
-
-on runs 37268729425 and 37269325567, and that single line cannot distinguish the
-two real causes. npm deliberately does not tell an unauthenticated caller whether a
-package exists, so **an unregistered trusted publisher is reported as 404, not as
-401 or 403.**
-
-Two failure surfaces were making that expensive to diagnose, and both now say so
-out loud. Neither changes what the workflow does; both only change what it prints.
-
-- **The publish step** now names the real cause when npm returns 404, states that
-  the package exists and the version is absent, prints the npmjs.com fields above,
-  and calls out the `npm publish` allowed-action requirement. A rejected or absent
-  token looks different (401, or `ENEEDAUTH`), and the step says that too.
-- **The version-existence gate** now warns, at the point where it would otherwise
-  tell someone to bump the version, that a 404 also means "unauthorized". Bumping
-  to escape a 404 consumes a release number on both registries and still will not
-  publish while the publisher is unregistered.
-
-Worth recording precisely: in **both** runs the version gate **passed**. The
-tarball built, provenance was signed and submitted to the Sigstore transparency
-log, and only the `PUT` failed. So both runs did prove the authentication failure,
-and the fix is the registration above — not a version bump.
-
-## [v2.2.4] - 2026-10-12
-
-### Housekeeping — release alignment
-
-- Publishes the post-2.2.3 repository state (single-shot automatic npm
-  publishing, #165) to PyPI and npm: the 2.2.3 upload predates that commit, so
-  both registries were one commit behind `main`. No behavioural change.
-
-## [v2.2.3] - 2026-10-05
-
-This release exists to exercise the OIDC trusted-publish path, now that the
-npmjs.com trusted publisher for `scientific-computing-system` is registered.
-
-The previous npm 2.2.2 was published in token mode and therefore carries no
-attestation. Nothing about the launcher changed: `src/` is untouched since
-2.2.2, and the only source change in this release is the version string itself.
-
-## [v2.2.2] - 2026-10-05
-
-Clears the last 17 open CodeQL alerts in this repository. None of them was a
-security vulnerability, and **none was a logic defect** — no discarded result, no
-missing `return`. Nothing is suppressed: there is no `# nosec`, no path exclusion
-and no `codeql.config` entry.
-
-### Behaviour change
-
-**One, and it is a removal:** the private path `cds.cli._parser._build_parser` no
-longer resolves.
-
-`_build_parser` was an alias for `build_parser`, kept for backwards
-compatibility. It was defined in `cds.cli._parser` but imported and re-exported by
-`cds.cli.__init__`, so within its own module it was genuinely unreferenced —
-which is exactly what `py/unused-global-variable` reported. The assignment has
-moved to `cds.cli.__init__`, beside its only consumer and inside the `__all__`
-that already exports it.
-
-- `cds.cli._build_parser` is unchanged: still present, still in `__all__`, still
-  the same object as `cds.cli.build_parser`. This is the documented
-  backwards-compatibility surface and it keeps working.
-- `cds.cli._parser._build_parser` is gone. Nothing in this repository referenced
-  it and the name is underscore-private, but a downstream script that reached
-  into the private submodule would break.
-
-There is now a test pinning the alias, because the original defect was that
-nothing asserted it existed.
-
-### Fixed
-
-- **Protocol placeholders are docstrings, not bare `...`.** Nine
-  `py/ineffectual-statement` alerts across `src/cds/ml/model_selection.py`,
-  `src/cds/ml/voting.py` and `src/cds/tools/adapters.py` were the conventional
-  `...` terminating a `typing.Protocol` method. These are false positives in the
-  strict sense: `...` is the documented placeholder for a structurally-typed
-  method whose implementation lives in the real backend module, and no code path
-  executes it. `SoftVotingModel` is the only `@runtime_checkable` one, and
-  `isinstance` against a runtime protocol inspects attribute *presence* without
-  calling the body.
-
-  They became docstrings rather than `pass` because coverage.py excludes an
-  ellipsis-only body but counts `pass`; measured, swapping it in drops those
-  lines from 100% to 75% and breaks the coverage gate. `raise NotImplementedError`
-  has the same coverage problem and would additionally change behaviour if the
-  body were ever reached. `src/cds` already contained nine docstring-only bodies
-  with no alert on any of them.
-
-- **`src/cds/tools/registry.py` imports `importlib` one way.** Three spellings
-  were mixed: `import importlib`, `import importlib.util` and
-  `from importlib import metadata`. The first was fully subsumed by the second.
-  Now `import importlib.metadata` and `import importlib.util`, with call sites
-  fully qualified. Four monkeypatch targets in `tests/` were retargeted to match.
-
-- **Four `py/unnecessary-lambda` alerts in the test suite.** `lambda x: max(x)`
-  and `lambda values: sum(values)` are plain wrappers around a callable; the
-  callables are now passed directly.
-
-- **`tests/test_fitting_bootstrap.py` imports `cds.modeling.fitting` one way.**
-  A module-level `from ... import` coexisted with function-local
-  `import ... as fitting`. The single `import ... as fitting` form is used now and
-  the module-level names are qualified through it.
-
-### Added
-
-- **`tests/test_protocol_placeholders.py`** pins the protocol bodies on the AST,
-  because a docstring-only body and a docstring followed by `pass` compile to
-  almost identical instructions and only the syntax tree tells them apart. It also
-  asserts the placeholder semantics (`None` when called unbound), that
-  `SoftVotingModel` is still a working structural contract, and that every
-  declared signature and annotation still resolves. Negative-controlled against
-  four mutations, all caught: docstring-plus-`pass`, `...` reinstated, body
-  replaced by a real statement, and a statement appended after the docstring.
-
-### Changed
-
-- README's pasted `cds --version` transcript now reads `System version 2.2.2`.
-  Every provenance and attestation statement in `README.md` and `SECURITY.md`
-  still refers to **2.2.1** deliberately: those describe the published release,
-  including its digests, and remain true until a newer one ships.
-
-
-### Fixed
-
-- **Provenance claims are now scoped, measured, and guarded.** A follow-up report
-  asserted that PyPI had no PEP 740 attestation either. Re-measured directly, that
-  is **not** the case, so the previous text was left standing and made precise
-  rather than weakened:
-
-  - PyPI **2.2.1** serves a PEP 740 provenance bundle for **both** the wheel and
-    the sdist (HTTP 200 on the per-file `/integrity/.../provenance` endpoint),
-    and each bundle's `subject` digest equals the `sha256` PyPI publishes for
-    that file. The 404 in the report came from requesting
-    `https://pypi.org/integrity/scientific-computing-system/2.2.1/`, which is a
-    directory, not the per-file endpoint.
-  - npm **2.2.1** has **no** attestation: the attestations endpoint returns 404.
-    This part of the report was correct.
-
-  The security posture is therefore unchanged and more precisely stated. What
-  changed: `SECURITY.md` now separates the three things that were being conflated
-  — a **PEP 740 attestation** (Sigstore-signed, attests *who built this*),
-  **npm `dist.signatures`** (registry transport signing, attests nothing about
-  the build), and a **content digest** (`sha256` on PyPI, `dist.integrity` on
-  npm; pins *which bytes*, not *where they came from*). It lists the published
-  digests to pin, gives the commands that verify them, and states the exact
-  trusted-publisher coordinates still to be registered for npm.
-
-- **Reproducible-build claim scoped to what was actually measured.** Two
-  consecutive builds of the same commit with the same pinned backend produced
-  byte-identical wheel and sdist. Those digests do **not** match the published
-  ones (the release runs a hash-locked Linux toolchain; the check ran elsewhere),
-  so the documentation now claims determinism for a fixed toolchain and
-  explicitly declines to claim the published artifacts are bit-for-bit
-  reproducible from source.
-
-- **npm launcher prerequisite re-verified.** With `cds` absent from `PATH`, the
-  shim proceeds straight to interpreter resolution (`python`/`python3`/`py`) and
-  runs `python -m cds`; it never looks for a `cds` console script. README,
-  `SECURITY.md` and the docs already agreed on this wording, and it is now
-  backed by an explicit check rather than by reading the source.
-
-### Added
-
-- `docs/checks/verify_provenance_claims.py` — a guard that parses the attestation
-  claims out of `README.md` and `SECURITY.md` and compares them against the live
-  registries, failing if the prose asserts something the registries contradict.
-  It also rejects prose that overstates `dist.integrity` as provenance or allows
-  the attested subject to differ from the published digest. Negative-controlled:
-  three false claims (PyPI not attested, npm attested, digest mismatch acceptable)
-  each turn it red. Wiring it into CI is left to the workflow owner; this change
-  is docs-only by scope.
-
-## [v2.2.1] - 2026-10-04
-
-Documentation and release-surface corrections. **No library behaviour change**:
-nothing under `src/cds/` was modified except the `__version__` constant, so no
-numerical kernel, public API signature or CLI subcommand differs from 2.2.0.
-
-The reason this patch release exists: `README.md` is the `long_description`, and
-PyPI only re-reads it when a new release is uploaded. 2.2.0 shipped the README as
-it stood before the truthfulness work below, so the PyPI project page for 2.2.0
-still advertises claims the repository has since retracted. Publishing 2.2.1 is
-what makes the corrected README the one PyPI renders.
-
-### Fixed
-
-- **README performance claim corrected to the committed artifact.** The "catch"
-  paragraph asserted "~0.05 s versus ~0.0001 s ... roughly 580x slower" and
-  described it as "this machine's benchmark run", while pointing readers at
-  `docs/benchmarks.md` for "the hardware they came from". `benchmarks/results.json`
-  actually records 0.0696 s versus 0.000060 s (**1154.8x**) at commit `7213425`,
-  and that same file records Platform / CPU / Python / NumPy as "not recorded"
-  with an explicit "treat the absolute timings as unverified" warning. The line
-  added by the earlier truthfulness commit therefore contradicted the warnings it
-  shipped alongside. Both the README and `docs/why-pure-python.md` now quote the
-  artifact's own numbers and state that the environment was not recorded.
-
-- **npm launcher prerequisite stated correctly.** README and `SECURITY.md` said
-  the `scs` shim works once `cds` is "on your PATH". `index.js` resolves an
-  interpreter (`python`/`python3`/`py`) and runs `python -m cds`; it never looks
-  for a console script on `PATH`. Corrected to "requires the Python distribution
-  installed so that `python -m cds` resolves".
-
-- **Stale version references left behind by the 2.2.1 bump.** The README's pasted
-  `cds --version` transcript still read `System version 2.2.0` after the version
-  moved, and `SECURITY.md` still recommended pinning `==2.2.0`. Since the README
-  is the `long_description`, that line would have shipped verbatim to the PyPI
-  project page. Both were re-derived from live commands at 2.2.1.
-
-  Every other pasted transcript was re-checked against the installed 2.2.1 wheel
-  and found current: the quickstart output (SVD singular values, damped-oscillator
-  final state, regression fit), `cds modules` printing 26 rows and omitting exactly
-  the nine documented modules, the structural claims (34 subpackages, 35 public
-  feature modules, 505 names / 342 functions / 163 classes), the benchmark ratio
-  against `benchmarks/results.json`, and all five documented extras.
-
-  Two further `SECURITY.md` claims were false and are corrected: `scs` was
-  documented as needing a `cds` console script on `PATH` when the launcher
-  resolves an interpreter and runs `python -m cds` (verified: the shim prints
-  `System version 2.2.1` with no `cds` on `PATH`), and the PyPI attestation cell
-  claimed a PEP 740 bundle for the published 2.2.0 when PyPI serves none.
-
-  The pin example is now version-agnostic by construction, so it cannot rot at
-  the next bump.
-
-- **Module-surface claims are now accurate.** "34 subpackages" silently omitted
-  the two top-level public modules (`causal.py`, `sensitivity.py`), and
-  "`cds modules` for the live list" was wrong twice over: that command prints a
-  curated 26-entry subset and omits `bayes`, `causal`, `core`, `fractals`,
-  `genetics`, `infotheory`, `interpolate`, `pde`, and `wavelets`. README,
-  `docs/api.md` and `docs/index.md` now state the real counts and flag
-  `cds modules` as a subset. The unsupported "46 public functions / 534 exports"
-  hero claim does not exist in the repository or in any reachable commit; the
-  README instead carries counts derived from the package itself (505 exports:
-  342 functions, 163 classes across 35 feature modules).
-
-- **Documentation no longer claims npm is unpublished.** npm 2.2.0 is live and
-  npm is a supported channel, but `README.md` line 41 still said "npm is no
-  longer published". Because `README.md` is listed in the npm `files` allowlist,
-  that sentence shipped **verbatim inside the published 2.2.0 tarball**, so the
-  npm package page contradicted its own README. `README.md`, `SECURITY.md` and
-  `docs/related.md` now describe both channels accurately; the npm version badge
-  is restored now that the registry and PyPI agree.
-
-- **A successful publish is no longer reported as a failure while npm is still
-  propagating it.** `npm publish` returns as soon as the registry accepts the
-  upload, but the version becomes readable on the read path asynchronously. The
-  post-publish check read once, immediately, and on run `37136131220` got
-  `npm error 404 No match found for version 2.2.0` — while 2.2.0 was in fact
-  published and recorded by the registry ninety seconds later. A maintainer
-  reading that run had every reason to believe the release had broken. Three
-  sibling repositories hit the same false failure.
-
-  The check now polls the registry with backoff over a budget of several minutes,
-  succeeds on the first match, and still fails closed if the version genuinely
-  never appears, emitting a `::warning::` first so a slow-but-successful publish
-  is never read as a hard failure.
-
-  It queries the registry's JSON API instead of `npm view`, which was a poor fit:
-  it reports "absent" and "denied" with the same `E404`, and it resolves against
-  the userconfig the job created for *writing*, so a read-only confirmation had no
-  reason to touch publish credentials at all. Both directions are exercised
-  against a stub registry, and the retry budget itself is asserted, since
-  shortening it to make a test fast is what caused the bug.
-
-- **The publish path is now guarded rather than merely enabled.** The launcher
-  contract test previously asserted that publishing stayed disabled, which would
-  have silently passed against a disabled workflow. It now asserts a real
-  `npm publish --provenance` invocation, `id-token: write`, the absence of
-  `private: true`, the absence of the disabled stub, and the presence of every
-  gate that makes a publish safe: the registry version-existence check, the
-  `npm pack --dry-run` tarball allowlist, and the npm/Python version lockstep.
-
-- **The npm toolchain version floor rejected a compliant toolchain.** The first
-  real publish run failed on this gate:
-
-  ```
-  npm --version | grep -Eq '^11\.(5[1-9]|[6-9][0-9])\.|^1[2-9]\.'
-  ::error::npm 11.5.1+ is required for OIDC trusted publishing
-  ```
-
-  On Node 24, setup-node installs npm **11.19.0**. The `[6-9][0-9]` alternative
-  covers minors 60-99, so `19` never matched and the gate failed on a toolchain
-  that meets the floor. A regex cannot express "greater than or equal to" for a
-  dotted version without enumerating every minor, which is exactly the mistake
-  that shipped. The gate now parses the version, strips any leading `v` and
-  prerelease suffix, and compares major/minor/patch as integers against 11.5.1.
-  The Node half of the same gate ignored the patch component: it compared only
-  major and minor, so `22.9.0` was accepted even though the documented floor is
-  22.14.0. Both halves now use the same integer comparison.
-
-- **Token-mode npm publish failed with `ENEEDAUTH` while holding a valid
-  secret.** The run reached `npm publish` with `NODE_AUTH_TOKEN` populated and
-  still got:
-
-  ```
-  npm error code ENEEDAUTH
-  npm error need auth This command requires you to be logged in to
-                        https://registry.npmjs.org/
-  ```
-
-  Root cause: `actions/setup-node` was configured without `registry-url`, so it
-  wrote no npm userconfig at all. `NODE_AUTH_TOKEN` on its own is inert — npm only
-  substitutes it into a credential when some userconfig maps
-  `//registry.npmjs.org/` to `${NODE_AUTH_TOKEN}`. With no such entry npm never
-  attempts authentication, which is why the failure was `ENEEDAUTH` (no
-  authentication attempted) rather than `E401` (attempted and rejected) even
-  though the secret was present and correct. The fix is
-  `registry-url: "https://registry.npmjs.org"` on `setup-node`.
-
-  Separately, the credential check lived inline inside the publish step, so its
-  failure text appeared in the log while `npm publish` was invoked anyway. It is
-  now its own step ahead of both publish steps, so a non-zero exit ends the job
-  before npm can run, and it covers the OIDC mode too (verifying the runner
-  actually granted `id-token: write`, which the previous version never checked).
-
-- **The `bin` map is now pinned by tests, so a broken launcher command cannot
-  ship silently.** The `npm warn publish "bin[scs]" script name bin/scs.js was
-  invalid and removed` message had been reported as a defect that would leave
-  the published package with no working `scs` command. **That report was wrong.**
-  npm normalises the redundant `./` prefix and ships the entry either way; the
-  packed tarball keeps `bin: { scs: "./bin/scs.js" }` alongside `bin/scs.js`, and
-  installing it creates `scs`, `scs.cmd` and `scs.ps1` and `scs --version`
-  succeeds. `axiomize@1.12.4`, published from the identical shape, ships the same
-  and is not deprecated. No `package.json` change is required.
-
-  What *is* a real hazard is the opposite: npm ships a `bin` pointing at a
-  missing file, or one excluded by `files`, with **no warning at all**. Five
-  tests now assert the bin map is a valid command-name to path mapping, that
-  every target exists and is covered by `files`, that the shim carries a `node`
-  shebang, and that the real tarball (`npm pack --dry-run --json`) still contains
-  both the shim and the bin entry. One further test documents that the `./`
-  prefix is intentional so the cosmetic warning is not "fixed" by a future
-  maintainer.
-
-### Added
-
-- **`tests/test_readme_surface.py`** derives the README's structural claims from
-  `src/cds/` and from the installed package: subpackage count, presence of both
-  top-level public modules, the export total, per-module table coverage, the
-  benchmark ratio against `benchmarks/results.json`, and a guard against
-  describing `cds modules` as exhaustive. This drift was previously invisible to
-  CI, which is how it survived several releases. Verified by mutation: five
-  separate re-introductions of the audited defects each turn the suite red.
-
-- **`codemeta.json` is now a locked version surface.** It was left out of the
-  original five surfaces and drifted: it still declared `2.1.0` after the package
-  reached 2.2.0, while every other surface had moved. CodeMeta is a
-  machine-readable publication record, so a stale `version` there advertises the
-  previous release to every automated consumer while the installed package
-  reports a different one. `scripts/check_version_lockstep.py` now reads it and
-  `tests/test_codemeta_version_lockstep.py` fails CI on drift. It is also added
-  to the sdist allowlist, without which that suite failed with `FileNotFoundError`
-  when run from an unpacked sdist.
-
-- README coverage: `cds.core` and `cds.graph` rows, `examples/` (35 runnable
-  files) and `dashboard/app.py` entries, all 13 CLI subcommands, the `[pandas]`
-  extra, `paper.md`/`paper.bib` (JOSS) and `codemeta.json`, and a Contributing
-  section with the `pip install -e ".[dev]"` / `pytest` / `mkdocs serve` loop and
-  the 100% blended-coverage gate. Duplicated prose was removed (the supply-chain
-  section now defers to `SECURITY.md` instead of restating it, and the generic
-  "Common use cases" filler is gone).
-
-- **Two supported npm publish modes**, selected by the `use_token_fallback`
-  dispatch input (boolean, default `false`):
-  - **OIDC trusted publishing** (preferred, default) — `id-token: write`,
-    `npm publish --provenance`. No registry secret involved.
-  - **Token mode** (`use_token_fallback=true`) — uses the repository's existing
-    `NPM_TOKEN` secret via `NODE_AUTH_TOKEN`. This is the mode in use while the
-    npmjs.com trusted-publisher registration is pending.
-
-  The token mode deliberately omits `--provenance`. Provenance is an OIDC-only
-  Sigstore attestation: a token cannot mint one, and npm rejects the
-  combination. The token mode prints a NOTICE that the release carries no
-  provenance rather than passing a flag that cannot work or implying an
-  attestation exists. Both modes are fail-closed: a requested mode with no usable
-  credential exits non-zero with an actionable message, and token mode never runs
-  automatically, so a broken OIDC configuration cannot silently downgrade to the
-  long-lived credential.
-
-### Changed
-
-- **npm publishing is real again.** This reverses two earlier decisions, both
-  deliberate at the time and recorded here so the history is not silently erased:
-  the decision in `52717c5` to disable npm publishing (which replaced the publish
-  step with `run: echo "npm publishing is disabled; PyPI is the install path" &&
-  exit 0`), and `"private": true` in `package.json`, added by `#140` while
-  publishing was disabled. `private: true` makes `npm publish` refuse to run at
-  all, so the flag had to go before the workflow could work. The `files` allowlist
-  is retained: it is what keeps the repository (tests, CI workflows, 10k+
-  statements of Python, promo media) out of the published tarball. The npm
-  channel is on OIDC trusted publishing (`id-token: write`,
-  `npm publish --provenance`); no long-lived registry token is used on the
-  primary path.
-
-- README shortened with **higher** coverage: the supply-chain section dropped from
-  209 lines to a 3-line summary plus a link, and "The catch" reduced to a short
-  paragraph.
-
-- **This release carries a PyPI attestation; 2.2.0 does not.** PyPI's JSON API
-  reports zero PEP 740 attestation bundles for 2.2.0, which went out in token
-  mode — a token cannot mint a Sigstore attestation. 2.2.1 is published by
-  `release.yml` through `pypa/gh-action-pypi-publish` with Trusted Publishing
-  (OIDC), so it will carry one, as long as the `pypi` environment's trusted
-  publisher is configured — a misconfiguration fails the publish loudly rather
-  than degrading silently.
-
-## [v2.2.0]
-
-Security hardening of the provenance path surface: provenance manifest paths
-are confined (`src/cds/_paths.py`), and the runtime dependency graph is guarded.
-No numerical kernel or public API signature changed. (Content owned by the
-security agent; this heading exists to satisfy the version-lockstep gate.)
-
-## [v2.1.0] - 2026-09-30
-
-Release-hardening pass covering the CI, quality-gate and packaging surface. No
-numerical kernel, public API signature or `cds` CLI subcommand changed.
-
-New public modules that first shipped in this release line (noted here because
-the release notes below cover only the hardening pass): `cds.validation`
-(cross-method verification, distribution-shift reporting), `cds.causal`
-(assumption-gated estimators — no causal-structure inference from observational
-correlation), `cds.sensitivity` (local and variance-based global sensitivity,
-identifiability), `cds.units` (SI dimensional analysis), `cds.workflow`
-(approval-gated, fail-closed orchestration), `cds.provenance` (manifests,
-hashing, checkpoints), `cds.data_io` (streaming I/O, optional HDF5/NetCDF),
-`cds.tools` (lazy optional-backend adapters), and `cds.uncertainty` (analytic
-and correlated Monte-Carlo propagation).
-
-### Fixed
-
-- **npm launcher (`index.js`, `bin/scs.js`)**: the published launcher could not be
-  parsed by Node (`SyntaxError: Unexpected token ';'`), and had it parsed it
-  spawned `python -m scs.cli`, a module that has never existed in any release
-  (the import name is `cds`). Both defects shipped in `1.0.0` on npm and were
-  invisible because `npm test` was a placeholder that exited 1 without running
-  anything. The launcher is now syntactically valid, targets `python -m cds`,
-  propagates the child's exit status, and reports one actionable message when no
-  interpreter is found.
-- **npm package contents**: `package.json` shipped no `files` allowlist, so a
-  publish would have uploaded the whole repository (tests, workflows, 10k+
-  statements of Python, promo media). Publication is now restricted to an
-  explicit allowlist.
-- **npm version drift**: `package.json` declared `1.0.0` while the Python
-  distribution was at `2.1.0`. It now tracks the Python version and CI fails on
-  any drift.
-- **Version-discipline bypass under rebase merges**
-  (`scripts/check_version_discipline.py --base-ref HEAD^1`): `HEAD^1` resolves to
-  the previous commit of the *same branch*, so in a multi-commit rebase merge only
-  the final commit's diff was inspected. A PR could change `src/cds/` in one
-  commit, follow with an unrelated commit, and pass the gate with no version bump
-  at all. The gate now diffs against the PR merge-base.
-- **Release fail-closed behaviour**: the publish job could report success after a
-  verification step had failed. That path is closed; every verification failure
-  now fails the job before any registry or tag mutation.
-- **Docs deployment ordering**: `deploy-docs` depended only on the `test` matrix,
-  so gh-pages could be updated from a run whose `audit`, `version_discipline` or
-  `test`-aggregate gates had failed. It now depends on the aggregate `CI` job.
-- **sdist test-suite failure**: `tests/test_release_contract.py` reads
-  `.github/workflows/*.yml`, which the sdist `only-include` list omitted, so the
-  shipped source distribution could not pass its own test suite (13 failures).
-  The CI workflow files are now part of the sdist.
-
-### Added
-
-- **`npm test` contract suite** (`npm.test.js`): assertions covering
-  `node --check` parseability, the `cds` module target, argument forwarding, exit
-  status propagation, the `files` allowlist, npm/Python version agreement, and a
-  guard that `npm-publish.yml` stays a disabled no-op. CI runs `npm run check`
-  and `npm test` on every push and pull request; **nothing in CI publishes to
-  a registry**.
-- **`scripts/check_version_lockstep.py`**: machine-enforced agreement across
-  `pyproject.toml`, `package.json`, `src/cds/_version.py`, `CITATION.cff`, the
-  runtime `cds.__version__` import, `CHANGELOG.md` and -- with `--dist-dir` --
-  the built wheel and sdist metadata. `2.1.0` had shipped to PyPI with no
-  `CHANGELOG.md` entry; that class of drift is now a red build.
-- **Wheel/sdist content assertions in CI**: the packaging job now asserts the
-  exact filename, distribution name, version, `py.typed` marker, sdist root
-  directory and the absence of forbidden paths (test fixtures, promo media,
-  `.github`, `site/`) rather than building artifacts and trusting them.
-- **Timeouts on every CI job** and per-job least-privilege `permissions:`.
-
-### Changed
-
-- All GitHub Actions references are pinned to full immutable commit SHAs;
-  previously several workflows used mutable `@v4` / `@v7` / `@v8` tags.
-- Branch ruleset for `main` extended in place (not replaced) to require the
-  aggregate `CI` check plus the `Installed CLI Smoke`, version-discipline,
-  packaging and npm contract jobs, and to dismiss stale reviews on push.
-- npm publishing stays disabled per product decision ("npm is no longer
-  published"; `npm-publish.yml` is a deliberate no-op). `package.json` is marked
-  `private`, the npm contract test asserts the workflow stays a no-op, and
-  nothing in CI uploads to a registry.
-- Removed the dead workflow files that main did not already remove:
-  `wsl-science-runner-smoke.yml` (targeted a self-hosted runner label with zero
-  registered runners). The retired `public-external-validation-p08-*` experiment
-  workflows and the one-shot `p08-cancel-noncanonical-runs.yml` /
-  `tmp-compassion-raw-acquire.yml` jobs were deleted on `main` directly and are
-  kept deleted here.
-
-## [v2.0.1] - 2026-09-29
-
-Metadata-only patch release for improved PyPI discoverability. No runtime API or numerical behavior changes.
-
-### Changed
-
-- Expanded PyPI keywords and classifiers for reproducibility, uncertainty quantification, sensitivity analysis, dimensional analysis, scientific workflows, ODE/PDE, and related scientific-computing searches.
-- Refreshed development lock versions required by the current security audit.
-- Normalized repository trailing whitespace required by pre-commit.
-
-
-### Added
-
-- **Random Forest classifier** (`cds.ml`): bagged CART trees with
-  bootstrap resampling and per-split feature randomization (`sqrt`/`log2`
-  / explicit count), fully deterministic under a seed.
-- **Metrics** (`cds.ml`): `accuracy`, `confusion_matrix`,
-  `precision_recall_f1`, `macro_prf`, regression `mse`/`mae`/`r2_score`,
-  and tie-aware rank-based `roc_auc`.
-- **Cross-validation** (`cds.ml.model_selection`): `k_fold_indices` and
-  `cross_val_score` over the shared estimator interface.
-- **Interpolation module** (`cds.interpolate`): `interp1d` (linear /
-  nearest) and `interp2d` (bilinear on regular grids).
-- **SVD** (`cds.math_utils`): one-sided Jacobi decomposition with
-  `svd`, `rank` and `condition_number`; full U/Vt factors.
-- **STFT / spectrogram** (`cds.signals`): Hann/Hamming windows, framed
-  zero-padded transforms reusing the radix-2 FFT, `STFTResult`.
-- **Gradient Boosting classifier** (`cds.ml`): logistic-loss boosted
-  regression trees with Newton leaf values; binary labels.
-- **Bootstrap confidence intervals** (`cds.stats`): percentile-method
-  `bootstrap_ci` and two-sample `bootstrap_diff_ci`.
-- **Metropolis-Hastings sampler** (`cds.montecarlo`): 1-D random-walk
-  MCMC with burn-in/thinning and acceptance-rate reporting.
-- **Symplectic integrators** (`cds.diffeq`): semi-implicit Euler and
-  velocity Verlet with forward/backward integration.
-- **Constrained optimization** (`cds.optimization`): projected gradient
-  descent for box bounds and quadratic-penalty constrained solves.
-- **Hypergeometric & negative-binomial distributions**
-  (`cds.probability`), pmf + cdf for both.
-- **TF-IDF ranked retrieval** (`cds.knowledge`): `rank_tfidf` across
-  concepts and notes with smoothed idf.
-- **Haar wavelet transform** (`cds.signals`): `dwt` / `idwt` /
-  `dwt_multi_level`, orthonormal with perfect reconstruction.
-- **PDE solvers** (`cds.pde`): explicit FTCS heat equation (Dirichlet /
-  Neumann, stability-guarded) and wave equation (CFL-guarded).
-- **Gaussian Naive Bayes** (`cds.ml`): log-space scoring with variance
-  smoothing.
-- **Correlation-mining engine** (`cds.hypothesis`): `mine_correlations`
-  turns numeric datasets into statistically tested, falsifiable
-  `Hypothesis` objects.
-- **Power analysis** (`cds.stats`): `power_t_test`,
-  `power_proportion_test` and `required_n_per_group` sample-size solver.
-- **VotingClassifier** (`cds.ml`): hard (majority vote) and soft
-  (averaged probabilities) ensembles over the shared estimator interface.
-- Four new runnable demos under `examples/`: interpolation, PDE,
-  ensemble showcase and the end-to-end discovery pipeline.
-- **PCA end-to-end demo** (`examples/pca_demo.py`): scaling vs raw
-  variance comparison, component selection, 2-D ASCII projection,
-  reconstruction error and train/test discipline, with a matching
-  tutorial (`docs/tutorials/pca_demo.md`).
-- **ML correctness reference table** (`scripts/verify_ml_reference.py`,
-  `docs/ml_reference.md`), LogisticRegression, DecisionTree, KMeans,
-  PCA and LinearRegression checked against scikit-learn 1.9.0 outputs
-  on a fixed seeded dataset; one-command, dependency-free verification.
-
-### Changed
-
-- `DecisionTreeClassifier` now accepts `max_features` and `seed` for
-  random-forest-style split randomization (default behavior unchanged).
-- The README now displays the sklearn-parity badge and links the ML
-  Reference table. (The matching `ml-reference` CI job is prepared but
-  not yet applied. It needs a push from a token with the `workflow`
-  OAuth scope; see the `backup/pre-reorder` branch.)
-
-## [v2.0.0] - 2026-09-05
-
-Scientific workflow platform release. Reorganises the project from a numerical
-methods library into a layered system that separates computation, analysis,
-scientific assurance, orchestration, and data handling.
-
-### Added
-
-- Uncertainty propagation, provenance capture, and tool discovery.
-- Dimensional analysis, domain checks, and scalable data I/O.
-- Scientific adapters, sensitivity analysis, and tool orchestration.
-- CLI catalog refreshed for the expanded module set.
-
-### Changed
-
-- The project is organised into explicit layers (compute / analysis /
-  assurance / orchestration / data) with dependencies pointing downward.
-- Release pipeline enforces a single publish authority.
-
-## [v1.6.2] - 2026-08-23
-
-Patch release carrying the PyPI deprecation tombstone for the former
-`cognitive-discovery-system` distribution name, pointing users at
-`scientific-computing-system`. No API change; the import name stayed `cds`.
-
-## [v1.6.1] - 2026-08-21
-
-A **patch** release completing the JSON round trip for core data models.
-
-### Added
-
-- **`cds.core`**: `Hypothesis.from_dict()`: the inverse of `to_dict()`.
-  CLI/JSON output can now be re-imported: enum strings are coerced back to
-  `Domain` / `HypothesisStatus`, ISO-8601 timestamps are parsed, and missing
-  optional keys fall back to constructor defaults. Invalid `status` values
-  raise `ValueError`.
-
-### Changed
-
-- Internal layering cleanup: shared special-function kernels moved to their
-  single home (`cds.math_utils.special`) so lower-level packages never depend
-  on higher-level ones; a suite-level import-direction guard enforces this.
-- `cds.cli` is now a package (`_style` / `_handlers` / `_parser`) with
-  identical behaviour; refreshed module descriptions in `cds modules`.
-
-## [v1.6.0] - 2026-08-21
-
-A **minor** release deepening the ML, probability, ODE, and optimization
-toolkits toward scikit-learn / SciPy teaching parity, still zero runtime
-dependencies, still 100% blended coverage.
-
-### Added
-
-- **`cds.ml`**: `KNeighborsClassifier` / `KNeighborsRegressor` (brute-force,
-  deterministic tie-breaking), `KMeans` (k-means++ seeding, seeded),
-  `DecisionTreeClassifier` (CART + Gini), `LogisticRegression` (stable-BCE
-  gradient descent, optional L2), `LinearRegression` (closed-form vector OLS
-  via normal equations), `PCA` (cyclic Jacobi eigen-solver, transform /
-  inverse_transform), `StandardScaler`, `train_test_split` (seeded)
-- **`cds.probability`**: chi-square and Student-t distributions
-  (`chi2_pdf/cdf/ppf`, `t_pdf/cdf/ppf`), `gamma_pdf` + `sample_gamma`
-  (Marsaglia–Tsang with shape<1 boost), `beta_pdf` + `sample_beta`
-  (exact gamma-ratio identity)
-- **`cds.diffeq`**: implicit stiff solvers: `backward_euler`,
-  `trapezoid_method` (Crank–Nicolson) and their `_system` variants; unified
-  θ-method core with Newton iteration over analytic or central-difference
-  Jacobians via the shared PLU solver
-- **`cds.optimization`**: `nelder_mead` simplex (degenerate-simplex and
-  symmetric false-convergence guards), `simulated_annealing` (Metropolis rule,
-  box bounds, seeded)
-- **`cds.stats`**: nonparametric tests: `mann_whitney_u` and
-  `wilcoxon_signed_rank` with tie/zero corrections (normal approximation)
-
-### Fixed
-
-- Test-suite pyplot figures are now closed per test, silencing matplotlib's
-  "more than 20 figures" memory warning in long sessions
-
-### Changed
-
-- README "Why CDS?" pitch strengthened with proof numbers and a cross-domain
-  snippet; stale counts/versions synced across metadata (19 modules)
-
-## [v1.5.0] - 2026-07-20
-
-A **minor** release expanding algorithms across graph theory, Monte Carlo,
-linear algebra, and CLI, still zero runtime dependencies.
-
-### Added
-
-- **`cds.graph`**: `degree`, `connected_components`, `bellman_ford`,
-  `floyd_warshall`, `prim_mst`
-- **`cds.montecarlo`**: `mc_expectation`, `hit_or_miss` (2-D area estimation)
-- **`cds.math_utils`**: `vector_norm`, `frobenius_norm`, `matrix_trace`
-- **CLI**: `cds integrate <sin|cos|exp|x2|unit> --a --b -n --method`
-
-## [v1.4.0] - 2026-07-20
-
-A **minor** release expanding core scientific APIs and CLI ergonomics.
-Zero runtime dependencies preserved.
-
-### Added
-
-- **`cds.probability`**: CDFs (`gaussian_cdf`, `uniform_cdf`, `exponential_cdf`),
-  `geometric_pmf`, samplers (`gaussian_sample` Box–Muller, `exponential_sample`,
-  `poisson_sample` Knuth)
-- **`cds.stats`**: `spearman_correlation` (midranks), `percentile`, `z_scores`
-- **`cds.scientific`**: constants `epsilon_0`, `g`, `mu_0`; formulas
-  `coulomb_force`, `centripetal_acceleration`, `pendulum_period`, `doppler_frequency`
-- **CLI**: `cds stats <nums>`, `cds sample <dist> -n N --seed …`
-
-### Changed
-
-- `cds info` no longer hardcodes a stale test count; module list includes modeling/knowledge/nlp
-
-## [v1.3.2] - 2026-07-20
-
-A **patch** release expanding the optional ``cds[plot]`` surface.
-
-### Added
-
-- **`cds.plot` charts**: `plot_multi_series`, `plot_scatter`, `plot_regression`
-  (OLS via `cds.stats`), `plot_power_spectrum` (via `cds.signals`),
-  `plot_seasonal_decompose` (4-panel), `plot_heatmap`, `plot_loss`,
-  `save_figure(..., close=)` helper; histogram gains ``density=``
-- **CLI**: `cds plot … --kind series|hist|acf --file out.png`
-
-### Changed
-
-- Docs / Cookbook / demo updated for the expanded plot API
-
-## [v1.3.1] - 2026-07-20
-
-A **patch** release. Fixes the console entry point so `cds` works after a
-plain PyPI install.
-
-### Fixed
-
-- **`[project.scripts]`**: entry point was `cds.cli:app` but the CLI exports
-  `main` (argparse). Installing from PyPI then raised
-  `ImportError: cannot import name 'app' from 'cds.cli'`. Now points to
-  `cds.cli:main`. `python -m cds` was already correct.
-
-## [v1.3.0] - 2026-07-20
-
-A **minor** release focused on **visualization and ergonomics**. Adds the
-optional ``cds[plot]`` matplotlib extra, a CLI PNG export path, a companion
-notebook, and documentation. The zero-dependency core is unchanged: matplotlib
-is only imported when a plot function runs (or when ``cds plot --file`` is
-used).
-
-### Added
-
-- **`cds.plot` optional package** (`src/cds/plot/`):
-  - `plot_series`, `plot_histogram`, `plot_waveform`, `plot_spectrum`
-  - `plot_acf` / PACF stems via `cds.stats` time-series helpers
-  - `plot_optimization_path` for 2-D optimizer trajectories
-  - Lazy matplotlib backend with install-hint `ImportError`
-- **Extra**: `pip install scientific-computing-system[plot]` (also in `[all]`)
-- **CLI**: `cds plot 1,2,3 --file out.png` saves a PNG when matplotlib is
-  installed; without `--file` the existing ASCII terminal plot remains
-- **Examples**: `examples/plot_demo.py`, `examples/plotting_notebook.ipynb`
-- **Docs**: Cookbook matplotlib section, API reference for `cds.plot`, README /
-  module tables, ROADMAP v1.3.0 track
-
-### Changed
-
-- CI main matrix installs `.[pandas,plot]` so optional bridges stay at 100%
-  coverage; minimal-deps job omits `cds/plot/*` like `pandas_io`
-- PyPI description mentions optional matplotlib plotting
-
-## [v1.2.3] - 2026-06-29
-
-A **patch** release. Fixes the release pipeline that silently broke every
-publish since v1.1.8.
-
-### Fixed
-
-- **Release workflow (`release.yml`)**: removed an invalid
-  `administration: write` entry from the `sync-about` job's `permissions:`
-  block. `administration` is not a valid `permissions:` key, so GitHub
-  rejected the entire workflow file as a "workflow file issue" before any
-  job could start, failing in 0s and leaving v1.1.9 onward without a PyPI
-  upload or GitHub Release. The About-sync step is now best-effort
-  (`continue-on-error: true`) since `gh repo edit` needs an admin REST
-  scope the default `GITHUB_TOKEN` can't grant; the repo description is
-  synced by hand on release.
-
-## [v1.2.2] - 2026-06-29
-
-A **patch** release. No code changes. Documentation-only refresh.
-
-### Changed
-
-- **README: removed pictographic emoji** from the top navigation row, the
-  callout blocks, the "Support the project" section heading, and the trailing
-  sign-off. Em dashes are preserved. Brings the README in line with the
-  emoji-free house style already applied to the docs and live PR bodies.
-- **`.gitignore`: ignore local promo-GIF QA scratch** (audit/compare/measure
-  scripts under `scripts/_*.py` and extracted frames under `assets/_qa_*/`),
-  which are one-off diagnostic tooling and were never meant to ship.
-
-## [v1.2.1] - 2026-06-28
-
-A **patch** release. No code changes. Metadata-only refresh to improve
-PyPI discoverability.
-
-### Changed
-
-- **Strengthened PyPI `description`**: the short one-liner now names all 18
-  domain modules (quantum circuits, ML, NLP, signal processing, optimization,
-  statistics & time-series, ODE solvers, Monte Carlo, symbolic math, knowledge
-  graphs, hypothesis generation) and states the zero-runtime-dependency
-  guarantee. Improves search-result relevance on PyPI.
-- **Expanded `keywords`** from 12 to 20 entries, aligning them with the GitHub
-  repository topics (added `machine-learning`, `nlp`, `numerical-integration`,
-  `knowledge-graph`, `symbolic-math`, `data-analysis`, `physics`,
-  `hypothesis-generation`, `numerical-methods`; dropped the redundant `fft`
-  in favour of the broader `signal-processing`).
-
-## [v1.2.0] - 2026-06-25
-
-A **minor** release. The theme is **horizontal expansion + hardening**: three
-new domain features (time-series analysis, signal-filter design, 2-D
-quadrature), an optional pandas interop extra, and a documentation overhaul
-(Cookbook, Architecture guide, expanded Tour). Plus numerical-stability fixes
-and a no-behavior-change refactor of the two largest source files.
-
-No existing public API is removed or renamed; the `cds[pandas]` adapter is
-gated behind an optional extra so the zero-dependency core is untouched.
-
-### Added
-
-- **`cds.stats`: time-series analysis** (`src/cds/stats/time_series.py`):
-  - `moving_average`, `exponential_smoothing`, `difference`, `seasonal_decompose`
-  - `autocorrelation_function` (sample ACF), `partial_autocorrelation_function` (PACF)
-  - `kpss_statistic` (stationarity test) and `ljung_box` (autocorrelation test),
-    both returning result objects with `.statistic` / `.p_value`
-  - Exported from the top-level `cds.stats` namespace.
-- **`cds.signals`: filter design** (`src/cds/signals/filters.py`):
-  - `butter_lowpass(order, cutoff)`: Butterworth IIR low-pass coefficient design
-  - `apply_filter(signal, coeffs)`: direct-form IIR application
-  - `moving_median(signal, window)`: order-statistic denoiser (edge-preserving)
-- **`cds.numerical_integration`: 2-D quadrature** (`src/cds/numerical_integration/`):
-  - `simpson_2d(f, ax, bx, ay, by, nx, ny)`: 2-D tensor-product Simpson rule
-  - `gaussian_quadrature_2d(f, ax, bx, ay, by, n)`: 2-D tensor-product Gauss-Legendre
-- **`cds[pandas]` optional extra** (`src/cds/data_analysis/pandas_io.py`):
-  - `to_dataframe(data_set)` / `from_dataframe(df)` round-trip a `DataSet` to/from
-    a `pandas.DataFrame`, guarded so importing `cds` never requires pandas.
-  - Declared as an optional dependency in `pyproject.toml` (`pandas = {version = ...}`).
-- **Documentation**:
-  - **`docs/cookbook.md`**: a new problem-oriented recipe book (~48 recipes, one
-    per concrete task), verified end-to-end against the real API by
-    `_verify_cookbook.py`.
-  - **`docs/ARCHITECTURE.md`**: layered module dependency graph and data flow.
-  - **Tour of Numerical Methods** expanded with 2-D quadrature, time-series, and
-    filter-design stops.
-  - `docs/index.md` Quick Navigation now links the Cookbook, Tour, and Architecture.
-
-### Changed
-
-- **`cds.modeling` refactor**: `expression.py` (708 lines) split into
-  `_base.py` (AST base classes, visitors) and `_nodes.py` (operator/leaf node
-  types). Pure reorganization; no public symbols moved or renamed.
-- **`cds.stats` refactor**: distribution functions (normal/t/chi²/F CDFs and
-  inverses) extracted from `hypothesis_tests.py` into the private
-  `_distributions.py`, with `__all__` declared so the re-exports pass
-  `mypy --strict`.
-
-### Fixed
-
-- **`cds.math_utils.linalg`: numerical stability of pivoting.** Pivoting now
-  uses a scale-relative threshold (`max(|row|) * epsilon`) instead of a fixed
-  absolute epsilon, and rejects exact-zero pivots at sub-normal matrix scales.
-  Prevents spurious singular-matrix errors and mis-pivoting on
-  small-magnitude matrices. No change to well-scaled inputs.
-- **`cds.stats`**: `__all__` declared so the `_distributions` re-exports are
-  recognized as intentional public surface under `mypy --strict`.
-- **Tests**: stabilized a flaky mean-homogeneity property test by anchoring on
-  an absolute tolerance instead of a relative one.
-
-## [v1.1.9] - 2026-06-24
-
-### Minor — effect-size measures for the statistics & hypothesis stack
-
-A backward-compatible feature release. Adds standardized **effect-size**
-measures to `cds.stats` so users can report the *magnitude* of an effect
-alongside its significance, closing the long-standing gap where a
-hypothesis test answered *"is there an effect?"* but not *"how large?"*.
-No existing API or behavior changes; all prior tests remain green.
-
-### Added
-
-- **`cds.stats`: effect-size measures** (`src/cds/stats/hypothesis_tests.py`):
-  - `cohens_d(group_a, group_b)`: Cohen's *d* standardized mean difference
-    between two samples (pooled-SD denominator).
-  - `eta_squared_from_f(f, df1, df2)`: η² proportion of variance explained
-    by group membership, derived from a one-way ANOVA *F* statistic.
-  - `cramers_v(contingency_table)`: Cramér's *V* association strength for
-    an *r* × *c* contingency table (χ²-based, normalized to `[0, 1]`).
-  All three functions are exported from the top-level `cds.stats` namespace and
-  documented in the tutorial (`docs/tutorials/hypothesis_tests_demo.md`).
-- **Tutorial section**: *"Effect sizes"* walkthrough in
-  `hypothesis_tests_demo.md` showing how `cohens_d` / `cramers_v` pair with
-  the existing `t_test` / `chi_square_independence` tests.
-- **Getting-started snippets** (EN + TR) and `docs/index.md` now surface the
-  effect-size functions in the Python-API quick-start and module table.
-
-### Documentation
-
-- README module table, `docs/index.md` Key Features & module description,
-  and the EN/TR getting-started guides now mention effect-size support.
-
-## [v1.1.8] - 2026-06-21
-
-### Patch — ODE backward integration bug fix
-
-A user-facing **bug-fix release**. Forward integration is byte-identical
-to v1.1.7; only the previously-broken `t_end < t0` case changes behavior.
-Includes corrected deep-verification scripts and a docs sync, no new
-modules, no API additions.
-
-### Fixed
-
-- **`diffeq.solvers`: backward integration silently returned only the
-  initial value.** The fixed-step (`euler`, `rk4`, `midpoint`) and
-  adaptive (`rk45`) ODE solvers, plus `solve_system`, used a forward-only
-  loop guard `while t < t_end - LOOP_EPSILON`. When `t_end < t0` the
-  guard was immediately `False`, so the solvers did nothing and returned
-  only `y0`. The integration direction is now derived from
-  `copysign(1.0, t_end - t0)` and applied as
-  `direction * min(dt, abs(t_end - t0))`; `dt` stays an unambiguous
-  positive magnitude and the loop guard becomes
-  `(t_end - t) * direction > LOOP_EPSILON`. A zero-length span
-  (`t_end == t0`) still skips the loop because `copysign(1, 0) == +1`.
-  For `rk45`, step size is tracked as an always-positive `h_mag` so the
-  shrink/grow/snap logic keeps its forward semantics in either direction.
-  7 new `TestBackwardIntegration` regression tests cover all five
-  solvers.
-
-- **`hypothesis.generator`: confidence overflow past `n >= 12`.** The
-  generated-confidence formula `0.45 + i*0.05` overflowed the
-  `Hypothesis.confidence` `le=1.0` constraint for 12+ hypotheses,
-  raising `ValidationError`. Now clamped to `min(0.9, 0.4 + i*0.05)`.
-
-### Changed (verification tooling)
-
-- **`scripts/verify_d1_numerics.py`, `verify_d2_edge_cases.py`,
-  `verify_d4_hypothesis.py`**, stale reference values/thresholds that
-  produced spurious failures against correct code: D1.3 Romberg
-  monotone-decrease check only asserted above `1e-13`; D1.4 RK45
-  singularity now uses `t_end=2.0` (past the pole) so `RuntimeError` is
-  genuinely triggered; D1.7/D1.2 odd-degree Gauss-Legendre exact
-  integral corrected to `0`; Simpson `O(h^4)` thresholds loosened to
-  match the method's order; D4.2 confidence expectation updated to the
-  clamped formula. All three scripts now report **0 failures**.
-
-### Documentation
-
-- README "recent improvements" → v1.1.8 ODE fix entry; ROADMAP marks
-  hatch-vcs / git-cliff as tried-and-abandoned with the real rollback
-  reasons; SECURITY supported-versions refresh; dashboard UX
-  touch-ups; nav/cross-ref drift. **No code or behavior changes.**
-
-## [v1.1.7] - 2026-06-20
-
-### Patch — PEP 639 SPDX license metadata
-
-A maintenance release with **no API or behavior changes**. Standardizes
-the license declaration so it is recognized as a valid SPDX identifier
-both on PyPI and in package metadata, and removes drift-prone
-hardcoded numbers from the README.
-
-### Changed
-
-- **`pyproject.toml`**: adopted [PEP 639](https://peps.python.org/pep-0639/):
-  replaced the legacy `license = {text = "MIT"}` table form with the
-  SPDX `license = "MIT"` expression plus `license-files = ["LICENSE"]`.
-  The wheel/sdist METADATA now emit `License-Expression: MIT` and
-  `License-File: LICENSE`, which PyPI and GitHub recognize as a valid
-  SPDX id (the old table form was not parsed, so the license read as
-  unrecognized). Removed the now-redundant `License :: OSI Approved ::
-  MIT License` classifier (deprecated under PEP 639; would trigger a
-  metadata warning).
-
-### Documentation
-
-- **`README.md`**: removed hardcoded, drift-prone numbers (version
-  tag, test count, module count) in favor of the existing PyPI / CI /
-  codecov badges, so the docs no longer go stale between releases.
-
-## [v1.1.6] - 2026-06-20
-
-### Patch — release pipeline fix (OIDC → scoped API token)
-
-A maintenance release with **no API or behavior changes**. Fixes the
-broken automated release pipeline: the previous Trusted Publishing (OIDC)
-path required a PyPI publisher configuration that was never set up, so
-the v1.1.5 tag push failed at the upload step with an `invalid-publisher`
-error. The pipeline now uses a scoped **PyPI API token** (stored as the
-`PYPI_API_TOKEN` repo secret), which is the sole publish authority.
-
-This is the first release actually published by the automated pipeline,
-v1.1.4 and v1.1.5 were uploaded manually before the pipeline existed.
-
-### Changed
-
-- **`release.yml`**: removed the `id-token: write` permission and the
-  Trusted Publishing path; publishes via `pypa/gh-action-pypi-publish`
-  with `password: ${{ secrets.PYPI_API_TOKEN }}`. The workflow now also
-  creates the GitHub Release (previously done by the local script).
-- **`scripts/publish.py`**: no longer uploads to PyPI or creates the
-  GitHub release. It now builds, verified the built version against the
-  tag, runs tests, and pushes the tag (which triggers CI). Removed the
-  `--skip-release` flag and the local `~/.pypi-token` handling.
-- **`pyproject.toml`**: dropped `twine` from the `[all]` and `[dev]`
-  extras (no longer needed locally).
-- **Version bump `1.1.5` → `1.1.6`** in `pyproject.toml`,
-  `src/cds/_version.py`, and `CITATION.cff`.
-
-### Documentation
-
-- **`README.md`** and **`docs/maintenance.md`**: updated the release
-  pipeline description to reflect the scoped-API-token flow and
-  `release.yml` as the sole publish authority.
-
-## [v1.1.5] - 2026-06-20
-
-### Patch — quality, type-safety, test depth, and a 100% coverage gate
-
-A patch release: no API changes, no behavior changes. A coordinated sweep
-of refactoring (type-safety, code deduplication), deeper testing
-(property-based invariants, shared fixtures), expanded documentation
-(tutorials, architecture guide), and a hardening of CI to enforce full
-blended coverage. The result is the cleanest, most thoroughly verified
-release to date: **17 modules, 1230 tests, and 100% code coverage
-(statement + branch)**.
-
-### Added
-
-- **Python 3.13 support**: added 3.13 to the CI test matrix and the
-  `pyproject.toml` classifiers; the full suite is now green on 3.10–3.13.
-- **Shared test fixtures**: `tests/conftest.py` plus `tests/test_core.py`
-  centralize reusable fixtures and core invariants, reducing duplication
-  across the suite.
-- **Property-based invariant suite (B5)**: a Hypothesis-driven test set
-  that exercises numerical invariants (associativity, identity,
-  round-trip) over generated inputs, catching edge cases that
-  example-based tests miss.
-- **Tutorials for optimization, signals, ML, and statistics (B3)**: new
-  guided walkthroughs under `docs/tutorials/` covering the four most-used
-  subsystems.
-- **Contributing architecture section (B4)**: `CONTRIBUTING.md` now
-  documents the module layout and the data flow between subsystems, with
-  stale cross-references fixed.
-- **`examples/modeling_demo.py`**: a new end-to-end example demonstrating
-  the modeling workflow referenced by the tutorials.
-
-### Changed
-
-- **Closed remaining `Any` type escapes**: the last untyped boundaries in
-  the core and hypothesis modules now carry concrete types; `mypy --strict`
-  stays green.
-- **Generic `OptResult`**: the optimization result type is now generic
-  over its scalar type, and the narrowing casts that worked around the old
-  concrete signature have been removed.
-- **Deduplicated scalar central-difference**: the scalar central-
-  difference implementation that existed in both `calculus` and
-  `optimization` is now shared from a single source.
-- **Version bump `1.1.4` → `1.1.5`** in `pyproject.toml`,
-  `src/cds/_version.py`, and `CITATION.cff`.
-
-### CI
-
-- **100% blended coverage gate**: CI now fails unless both statement and
-  branch coverage reach 100%, locking in the coverage level as a
-  non-regression boundary.
-- **Regenerated benchmark report**: the benchmark report and
-  `results.json` were regenerated against the current codebase.
-
-### Documentation
-
-- **Synced stale test count and coverage**: corrected the documented test
-  count (1165 → 1230) and coverage figure (~99.6% → 100%) to match CI.
-- **Roadmap items shipped**: roadmap entries #2 (modeling) and #3
-  (knowledge organization) are marked released; the corresponding issues
-  are closed.
-
-## [v1.1.4] - 2026-06-19
-
-### Patch — documentation, CI, and housekeeping cleanup
-
-A patch release: no API changes, no behavior changes. Removes cosmetic
-distractions (emojis, sprint references) from issue templates and docs,
-fixes CI workflow schemas, and deletes ~3 500 lines of no-op autograd
-shim code that was never exercised at runtime.
-
-### Changed
-
-- **Issue templates**: removed decorative emojis from
-  `bug_report.md`, `config.yml`, and `changelog.yml` for a cleaner,
-  more professional appearance.
-- **`.github/labeler.yml`**: migrated to the `actions/labeler` v5
-  configuration schema (`triage` → `labels` key).
-- **`.github/workflows/changelog.yml`**: fixed a missing trailing
-  newline flagged by lint checks.
-- **Documentation**: stripped sprint-tracking references and
-  ephemeral planning files (`docs/superpowers/plans/`,
-  `docs/superpowers/specs/`); unified inline-code formatting across
-  tutorials and case-study pages.
-- **Removed no-op autograd shims**: deleted `src/cds/nlp/autograd/`
-  shim functions (`_grad.py` stubs, pass-through wrappers in
-  `ops.py` and `tensor.py`) that were placeholders and never
-  participated in any real gradient computation. ~3 500 lines removed.
-- **Examples**: aligned `ruff` formatting in
-  `examples/data_analysis_demo.py` and
-  `examples/ml_and_viz_demo.py`.
-- **Version bump `1.1.3` → `1.1.4`** in `pyproject.toml`,
-  `src/cds/_version.py`, and `CITATION.cff`.
-
-## [v1.1.3] - 2026-06-19
-
-### Patch — type-safety cleanup
-
-A patch release: no API changes, no behavior changes. Resolves the final
-block of `mypy --strict` errors so the type checker reports **0 errors
-across 136 files**. No public surface changed; all 1165 tests pass and
-the suite is unchanged.
-
-### Fixed
-
-- **43 `mypy --strict` errors resolved** across `examples/`, `dashboard/`,
-  and `scripts/`. The fixes fall into five categories, none of which
-  alter runtime behavior:
-  - **`int` → `float` argument types**: numeric literals passed to APIs
-    typed as `float` (e.g. integration tolerances, attention scaling)
-    now use explicit `float` literals so the call matches the signature.
-  - **`Domain` enum usage**: iteration and membership checks against the
-    `Domain` enum now go through `Domain.__members__.values()` / explicit
-    member references, matching the pattern established in v1.1.2 for
-    CodeQL compatibility.
-  - **Attention tensor rank**: reshape/transpose calls in
-    `examples/nlp_attention_demo.py` and `examples/nlp_mini_gpt_demo.py`
-    annotated to reflect the actual tensor rank rather than an
-    over-narrow `Any`/scalar guess.
-  - **Invariant list widening**: a few demo helper functions that
-    return heterogeneous sequences now declare `list[object]` (or the
-    specific union) instead of an impossible precise element type.
-  - **`Protocol` signature alignment**: a duck-typed callback protocol
-    in `scripts/publish.py` had a signature that diverged from its
-    concrete implementations; the protocol and call sites now agree.
-
-### Changed
-
-- **Version bump `1.1.2` → `1.1.3`** in `pyproject.toml` and
-  `src/cds/_version.py`.
-
-## [v1.1.2] - 2026-06-19
-
-### Patch — security hardening & CodeQL closure
-
-A patch release: no API changes, no behavior changes. Closes the remaining
-CodeQL code-scanning alerts with a fix (not a workaround),
-tightens `main` branch protection, and improves the discoverability of the
-vulnerability-reporting flow. Brings the repo to **0 open** code-scanning
-alerts (22/22 closed: 20 fixed by code, 2 dismissed as documented false
-positives).
-
-### Security
-
-- **CodeQL `py/non-iterable-in-for-loop`: fix.** Enum iteration
-  in `examples/core_demo.py` and `tests/test_hypothesis.py` now uses
-  `Domain.__members__.values()` instead of `for x in Domain:`. This is the
-  Enum API's standard member-collection view: functionally identical (same
-  members, same insertion order, all 1164 tests pass) but the return type
-  is an explicitly iterable mapping view that CodeQL's type resolver can
-  follow. Previous attempts (idiomatic iteration, direct import from the
-  defining module) did not satisfy the analyzer; this does, with no
-  camouflage (`list()` wrapping) and no behavior change.
-- **`main` branch protection strengthened.** Added `required_status_checks`
-  for `CI` and `CodeQL`, a PR can no longer merge into `main` while those
-  checks are red. `enforce_admins` is left disabled so the maintainer
-  retains a direct-push path; everything else (linear history, conversation
-  resolution, no force-pushes, no deletions) is unchanged.
-- **Security-reporting guidance.** The README now links to `SECURITY.md`
-  and the private-advisory flow; the bug-report issue template warns against
-  opening public issues for vulnerabilities and redirects to private
-  advisories.
-
-### Changed
-
-- **`CITATION.cff` version refresh.** Two stale `1.1.0` references (root and
-  `preferred-citation` blocks) bumped to `1.1.2`. This was missed in v1.1.1.
-
-## [v1.1.1] - 2026-06-19
-
-### Patch — supply-chain & CI hardening
-
-A patch release: no API changes, no behavior changes. Strengthens release
-integrity and CI correctness so downstream consumers and contributors get
-verifiable, low-churn workflows.
-
-### Security
-
-- **CodeQL static analysis** (`codeql.yml`): runs `security-and-quality`
-  query pack on every push/PR into `main` plus a weekly schedule; findings
-  surface as code-scanning alerts under the Security tab. Complements
-  `attest.yml` (which signs release artifacts with build provenance) and
-  `dependabot.yml` (dependency CVEs).
-- **README security badge**: live CodeQL status added next to the CI badge.
-
-### Changed
-
-- **`changelog.yml` made idempotent**: all dispatches now target a single
-  fixed branch (`chore/changelog-regen`); `peter-evans/create-pull-request`
-  updates the existing open PR instead of opening a duplicate per tag.
-  Previously up to 6 stale changelog PRs accumulated; now only one is ever
-  open. Also bumped the action `v6 → v7` and added a `concurrency` group to
-  serialize simultaneous dispatches.
-- **`benchmarks.yml` respects branch protection**: switched from a direct
-  bot push (rejected on protected `main`) to opening a PR via
-  `peter-evans/create-pull-request@v7`, so regenerated artifacts merge
-  through the normal review flow without breaking protection rules.
-
-### Removed
-
-- 6 stale auto-generated changelog PRs (#10, #19, #20, #21, #22, #23) and
-  their per-tag branches, all superseded by the hand-curated CHANGELOG on
-  `main`.
-
-## [v1.1.0] - 2026-06-19
-
-### Minor — two new modules (symbolic math + knowledge organization)
-
-A backward-compatible feature release. Adds two new public subpackages
-(`cds.modeling`, `cds.knowledge`) without changing any existing API. The
-platform now spans **17 modules**, **1164 tests**, and **99.59%** coverage.
-
-### Added
-
-- **`cds.modeling`**: symbolic algebra for equation development:
-  - An expression tree (`+`, `-`, `*`, `/`, `**`, unary `-`, variables,
-    numbers) built by overloading Python operators on a `Variable`/`Constant`
-    AST.
-  - Symbolic differentiation (`diff`), algebraic simplification
-    (`simplify`), substitution (`subs`), evaluation (`evaluate`), and
-    LaTeX export (`to_latex`).
-  - A `MathModel` for equation systems with `solve_equation` (Newton-Raphson
-    root finding) and `fit_parameters` (least-squares parameter fitting to
-    observations).
-  - Runnable demo (`examples/modeling_demo.py`) + tutorial.
-- **`cds.knowledge`**: a knowledge-organization layer in three pure-Python,
-  dependency-free files:
-  - `graph.py`: `Concept`, `Relation` (typed directed edges), and a
-    `KnowledgeGraph` with undirected traversal (shortest path via BFS,
-    transitive closure, cycle detection), neighbors, and JSON persistence.
-  - `notes.py`: `Note` + `Notebook` research notebook with tag and
-    concept lookups, and JSON persistence.
-  - `retrieval.py`: `search()` producing ranked `SearchResult` hits across
-    both concepts and notes (matched field + normalized score).
-  - Runnable demo (`examples/knowledge_demo.py`) + tutorial.
-- Both modules are wired into the package `__all__`, the CLI `modules`
-  listing, and the API reference (`docs/api.md`).
-
-### Maintenance
-
-- Docs: resync README, `docs/index.md`, getting-started (EN + TR), and
-  CITATION.cff to v1.1.0, module count 16→17, test count 883→1164,
-  coverage 99.48%→99.59%. Keep `pyproject.toml` + `src/cds/_version.py`
-  lockstepped at 1.1.0.
-- Chore(repo): ignore the `_demo_*.json` runtime artifacts the
-  knowledge demo writes next to its script, so a demo run no longer
-  dirties the working tree.
-
-## [v1.0.4] - 2026-06-18
-
-### Security & Tooling — CI hardening
-
-A follow-up patch to v1.0.3. No behavior changes to the published package;
-fully backward compatible. Adds continuous dependency-vulnerability scanning
-to CI, tightens the type-check configuration, and resynchronizes docs that
-had drifted after v1.0.0.
-
-### Maintenance
-
-- Chore(ci): add a `pip-audit` job to the CI workflow (`tests.yml`). Runs
-  once on the reference cell (Linux + Python 3.12) against the PyPI Advisory
-  database. Currently `continue-on-error: true`, the dev/docs/test toolchain
-  (jupyter, mkdocs, build, twine, pillow, lxml, ...) carries transitive deps
-  with open CVEs unrelated to the published runtime (typer/pydantic/rich,
-  which audit clean). Surfacing them every run gives visibility without
-  red-flashing the matrix on a fresh advisory.
-- Chore(types): remove the global `ignore_missing_imports = true` from
-  `[tool.mypy]`. CDS only depends on PEP 561 typed runtime libs (typer,
-  pydantic, rich), all of which resolve cleanly under strict mypy (98 files,
-  0 errors). Dropping the escape hatch means a future un-stubbed dependency
-  surfaces a real error instead of being silently typed as `Any`.
-- Chore(repo): delete a stray Windows `nul` artifact left in the working tree.
-- Docs: resync README + `docs/` after v1.0.0: test count 845→878, version
-  strings updated, `CITATION.cff` bumped to 1.0.4. Keep `pyproject.toml` +
-  `src/cds/_version.py` lockstepped at 1.0.4.
-
-## [v1.0.3] - 2026-06-18
-
-### Hygiene — test-suite type correctness
-
-A follow-up patch to v1.0.2. No behavior changes to the published package;
-fully backward compatible. Brings `tests/` to the same mypy baseline as
-`src/` so the full type-check (`mypy src/ tests/`) is green, and resolves
-post-release lint/test/publish findings caught after v1.0.2 shipped.
-
-### Testing
-
-- Test(types): clear all remaining mypy errors across `tests/` (39 files,
-  0 errors). Fixes list-variance issues (`Parameter <: Tensor`), redundant
-  `type: ignore` comments, and intentional error-path `**` operands.
-- Test(benchmarks): isolate benchmark test artifacts: `run_all()` /
-  `_write_json()` accept an `output_dir` parameter so `pytest` no longer
-  clobbers the committed `benchmarks/results.json`.
-
-### Maintenance
-
-- Chore(ci): resolve post-1.0.2 lint/test/publish findings (commit 5e429ec).
-- Docs: keep `pyproject.toml` + `src/cds/_version.py` lockstepped at 1.0.3.
-
-## [v1.0.2] - 2026-06-18
-
-### Hygiene — test isolation for benchmark artifacts
-
-A follow-up patch to v1.0.1. No behavior changes to the published package;
-fully backward compatible. Resolves a repo-hygiene issue where running the
-benchmark test suite silently clobbered the committed
-`benchmarks/results.json` artifact (and `docs/benchmarks.md`) on every
-`pytest` invocation.
-
-### Bug Fixes
-
-- Fix(tests): `test_run_all_generates_report` no longer writes into the
-  working tree. `run_all()` and `_write_json()` now accept an optional
-  `output_dir` parameter; the test passes its `tmp_path`, so the committed
-  `benchmarks/results.json` and `docs/benchmarks.md` are never modified by a
-  test run. Verified: object hash of `results.json` is byte-identical before
-  and after `pytest`.
-
-### Testing
-
-- Test(benchmarks): added a regression assertion that `results.json` lands
-  in `tmp_path` (not `benchmarks/`) after `run_all(output_dir=...)`.
-
-### Features
-
-- Feat(benchmarks): `run_all(output_dir=None)` and
-  `_write_json(record, output_dir=None)`, new optional parameter for
-  redirecting artifact output. Defaults preserve existing CLI behaviour.
-
-## [v1.0.1] - 2026-06-18
-
-### Maintenance — typed, documented, hardened
-
-A follow-up to the v1.0 stable release focused on packaging quality and
-numerical correctness guarantees. No behavior changes; fully backward
-compatible.
-
-### Features
-
-- Feat(packaging): declare PEP 561 type information: ship `src/cds/py.typed`
-  marker and force-include it in the wheel so downstream users get full
-  static type-checking support out of the box.
-- Feat(docs): add "type checked" badge to the README.
-
-### Testing
-
-- Test(invariants): add `tests/test_numerical_invariants.py`: 32
-  property-based numerical invariants across 8 modules (linalg, signals,
-  stats, quadrature, quantum, diffeq, monte carlo, probability). Fixed
-  seed, fully reproducible, zero new dev dependencies.
-
-### Documentation
-
-- Docs(api): add docstrings to all 51 previously-undocumented public
-  functions identified via AST scan (3 empty-docstring gaps closed).
-
-### Bug Fixes
-
-- Chore: bump version to 1.0.1.
-
-## [v1.0.0] - 2026-06-18
-
-### 1.0 — Stable release
-
-Cognitive Discovery Platform reaches its first stable release. All five
-subsystems of the v1.0 completion spec are implemented, gated, and
-verified: 99.16% statement coverage (845 tests passing), zero mypy
-errors, clean ruff, and a strict mkdocs build.
-
-### Features
-
-- Feat(nlp): NLP visualisation module: attention heatmap, PCA projection, training curve ([7956597](7956597))
-- Feat(benchmarks): emit results.json with timestamp + git SHA provenance, add CI workflow ([4e18500](4e18500))
-
-### Testing
-
-- Test(coverage): close NLP edge-case gaps: tensor/ops/optim/bpe/layers/model/attention; reach 99.16% statement coverage ([6f0a487](6f0a487))
-- Style(tests): ruff format cleanup: collapse over-split listcomp, expand train() signature, remove duplicate inline imports ([36f4ee4](36f4ee4))
-
-### Documentation
-
-- Docs(examples): add 9 module demos + matching tutorials ([9f00fc5](9f00fc5))
-- Docs(api): restructure mkdocs nav, add api.md lead-ins, fix stale test counts ([4cad8be](4cad8be))
-- Docs(nlp): fix griffe warnings: split combined params in docstrings ([3aedff4](3aedff4))
-- Docs(benchmarks): regenerate results.json with current SHA provenance ([69c5a88](69c5a88))
-
-### Bug Fixes
-
-- Chore: bump version to 1.0.0 + Production/Stable classifier; sync _version.py
-
-### Other
-
-- Promoted from `Development Status :: 4 - Beta` to `Development Status :: 5 - Production/Stable`.
-
-## [v0.10.0b1] - 2026-06-17
-
-
-### Features
-
-
-- Feat(nlp): autograd engine + MiniGPT-from-scratch ([5e0d308](5e0d308))
-
-
-### Documentation
-
-
-- Docs(changelog): regenerate for v0.9.0b8 (#17) ([2b0a7d3](2b0a7d3))
-
-
-## [v0.9.0b8] - 2026-06-17
-
-
-### Features
-
-
-- Feat(nlp): add multi-head attention + transformer block ([4f38cae](4f38cae))
-
-
-### Documentation
-
-
-- Docs(changelog): regenerate for v0.9.0b7 (#16) ([44ec93c](44ec93c))
-
-
-## [v0.9.0b7] - 2026-06-17
-
-
-### Bug Fixes
-
-
-- Fix: catch two more stale surfaces (CITATION.cff, mkdocs api.md) ([b59b6e3](b59b6e3))
-
-
-### Documentation
-
-
-- Docs(changelog): regenerate for v0.9.0b6 (#15) ([e1244ce](e1244ce))
-
-
-## [v0.9.0b6] - 2026-06-17
-
-
-### Bug Fixes
-
-
-- Fix: sync test count 572 to 655 across all surfaces ([952ffe0](952ffe0))
-
-
-### Documentation
-
-
-- Docs(changelog): regenerate for v0.9.0b5 (#14) ([f7a037b](f7a037b))
-
-
-## [v0.9.0b5] - 2026-06-17
-
-
-### Features
-
-
-- Feat(nlp): add cds.nlp module: BPE tokenizer + sinusoidal embeddings ([045b9d1](045b9d1))
-
-
-### Other
-
-
-- Build: drop hatch-vcs + setuptools_scm, switch to static versioning ([6e04d31](6e04d31))
-
-
-### Documentation
-
-
-- Docs(changelog): regenerate for v0.9.0b4 (#13) ([da52ee0](da52ee0))
-
-
-## [v0.9.0b4] - 2026-06-17
-
-
-### Bug Fixes
-
-
-- Fix: drop stale 'auditor' comment + sync 570 to 572 across docs and cli ([0dcaba6](0dcaba6))
-
-
-### Documentation
-
-
-- Docs(changelog): regenerate for v0.9.0b4 (#11) ([b1eda78](b1eda78))
-
-
-## [v0.9.0b3] - 2026-06-17
-
-
-### Bug Fixes
-
-
-- Fix(docs): include getting-started.tr.md in mkdocs nav; fix broken CONTRIBUTING link ([85316fe](85316fe))
-
-- Fix: bump CITATION.cff top-level version to 0.9.0b2 ([80cc3b4](80cc3b4))
-
-- Fix: bump CITATION.cff top-level version to 0.9.0b2 (was 0.8.5, missed during release) ([adee53c](adee53c))
-
-- Fix: keep cast() in test_legendre (Python 3.10/3.11 mypy needs it, 3.12 ignores) ([bcd20fc](bcd20fc))
-
-- Fix: resolve 34 mypy errors (matrix/fft type unions, plot float types, missing confidence arg, cli.Path) ([eea36a3](eea36a3))
-
-- Fix: type local _legendre import as Callable[[int, float], tuple[float, float]] (cross-Python mypy fix) ([486bad5](486bad5))
-
-- Fix: use # type: ignore[no-any-return] instead of cast() for cross-Python compat ([bd3aaa8](bd3aaa8))
-
-
-### Other
-
-
-- Build: add setuptools_scm local-scheme config (no-local-version, fallback) ([82d07c9](82d07c9))
-
-- Build: exclude hatch-vcs generated _version.py from ruff ([76760d3](76760d3))
-
-- Build: publish.py ignores hatch-vcs regenerated _version.py in dirty check ([bea5f71](bea5f71))
-
-- Build: setuptools_scm version_scheme=no-guess-dev; fix wheel version regex ([8ccb292](8ccb292))
-
-- Release: v0.9.0b1 - Beta milestone, CI multi-OS, hatch-vcs, git-cliff, attestation ([3e3928f](3e3928f))
-
-- Release: v0.9.0b2 - same code, re-tag to trigger attest workflow (checkout fix) ([c54e900](c54e900))
-
-- Release: v0.9.0b3 - branch protection, threat model, i18n, signed commits guide ([31983fe](31983fe))
-
-
-### Documentation
-
-
-- Docs(changelog): regenerate for v0.9.0b1 ([44f7823](44f7823))
-
-- Docs(changelog): regenerate for v0.9.0b2 ([404532c](404532c))
-
-- Docs(changelog): regenerate for v0.9.0b3 (#8) ([3a8ef95](3a8ef95))
-
-- Docs(changelog): regenerate for v0.9.0b3 (#9) ([c4fcb9b](c4fcb9b))
-
-- Docs: add threat model, signed commits guide, Why CDS comparison, Turkish i18n; update ROADMAP ([0ba07cf](0ba07cf))
-
-- Docs: update SECURITY.md supported versions (0.6.x → 0.8.x) ([b42cf5f](b42cf5f))
-
-
-### Styling
-
-
-- Style: pre-commit auto-fix (trailing whitespace, import order, ruff format) ([9adbf5a](9adbf5a))
-
-- Style: pre-commit auto-fix _version.py (add blank line before __version__) ([277b535](277b535))
-
-
-### Miscellaneous Tasks
-
-
-- Ci: changelog PR action needs explicit base branch (checked out on tag) ([b96d322](b96d322))
-
-- Ci: changelog action checks out main (not tag) to avoid detached HEAD issues ([af3cd12](af3cd12))
-
-- Ci: changelog workflow needs write contents + pull-requests perms ([a319a9f](a319a9f))
-
-- Ci: changelog workflow uses PR instead of direct push (branch protection compat) ([3f593cb](3f593cb))
-
-- Ci: fix attest + changelog workflows (checkout step, detached HEAD push) ([d2c9d6e](d2c9d6e))
-
-- Ci: quote step name with colon (YAML parse error) ([0731ca8](0731ca8))
-
-- Ci: rewrite tests.yml with simple bash conditional (no GitHub conditional parse issues) ([2cc8483](2cc8483))
-
-- Ci: split test step into 2 by matrix (gate vs report-only) - fix missing fi ([9e68ff0](9e68ff0))
-
-
-## [v0.8.5] - 2026-06-16
-
-
-### Other
-
-
-- Release: v0.8.5 - cds[all] extras, auto-generated API ref, docs deploy ([12b03b0](12b03b0))
-
-
-## [v0.8.4] - 2026-06-16
-
-
-### Other
-
-
-- Release: v0.8.4 - pydantic upgrade ([58ee8d9](58ee8d9))
-
-
-## [v0.8.3] - 2026-06-16
-
-
-### Other
-
-
-- Release: v0.8.3 - example guard consistency ([5017680](5017680))
-
-
-## [v0.8.2] - 2026-06-16
-
-
-### Other
-
-
-- Release: v0.8.2 - docstrings, knowledge/ removal, CHANGELOG backfill ([f22150c](f22150c))
-
-- Scripts: replace publish.ps1 with pure-Python publish.py ([c7c08e2](c7c08e2))
-
-
-### Miscellaneous Tasks
-
-
-- Ci: fix pre-commit and coverage gate for stable CI ([ca66c9f](ca66c9f))
-
-- Ci: remove Docs workflow; relax coverage gate; re-enable legacy Pages ([cdcf5d0](cdcf5d0))
-
-
-## [v0.8.1] - 2026-06-16
-
-
-### Other
-
-
-- Release: v0.8.1 ([4dc49e2](4dc49e2))
-
-
-### Documentation
-
-
-- Docs(roadmap): link open enhancement issues #2 and #3 under Longer Term ([ee6103b](ee6103b))
-
-- Docs: mark v0.8.0 as released; move 3 pending perf items to v0.8.1 ([80e6afe](80e6afe))
-
-
-### Testing
-
-
-- Test: hit 100% statement coverage; keep branch coverage off ([5c606c4](5c606c4))
-
-
-### Miscellaneous Tasks
-
-
-- Ci(pypi): fix pypi-publish workflow ([8335cb6](8335cb6))
-
-- Ci(scripts): add publish.ps1 for local PyPI releases ([57e81a4](57e81a4))
-
-- Ci: harden repo to 10/10 - pre-commit, lockfiles, coverage gate ([7c3b18f](7c3b18f))
-
-- Ci: remove pypi-publish workflow ([043b7f5](043b7f5))
-
-
-## [v0.8.0] - 2026-06-16
-
-
-### Other
-
-
-- Squashed: collapse 108 commits into a single cohesive history ([d4e8aee](d4e8aee))
-
-- Release: v0.8.0 - Performance & Benchmarks ([83211ef](83211ef))
-
-
-<!-- generated by git-cliff -->
+# Changelog
+
+All notable changes to **scientific-computing-system** will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [v2.2.8] - 2026-10-17
+
+### Scientific validation fail-closed thresholds
+
+- Reject NaN and infinite tolerances for independent-method agreement and conservation.
+- Reject non-finite OOD margins, distribution-drift thresholds, and residual diagnostic limits.
+- Add regression coverage for these parameter-contract failures and align the public
+  version tuple with the synchronized release metadata.
+
+## [v2.2.7] - 2026-10-15
+
+### Housekeeping — version lockstep
+
+- Release 2.2.7 (2026-10-15): records the production/Stable line against
+  which the repository's locked surfaces (codemeta.json, pyproject.toml,
+  package.json, `cds --version`) are verified by
+  `tests/test_codemeta_version_lockstep.py`.
+- Bumps the npm shim to the same 2.2.7 line so both publish channels ship
+  at identical versions, as documented in the README "Install" section.
+
+## [v2.2.6] - 2026-10-13
+
+### Housekeeping — second-round neighbour sweep
+
+- `transpose` shares the ragged-input contract the rest of the matrix API has
+  held since 2.2.5. It indexed only the leading row's width, so a short row
+  lost entries silently (`[[1.0],[2.0,3.0]]` became `[[1.0, 2.0]]`): the
+  result described a matrix nobody supplied. It now fails closed through the
+  same `_require_rectangular` check `mat_mul` and Cholesky use.
+- Geometric PMF boundary pinned: `geometric_pmf(0, p)` is 0 (no trial counted
+  1-based), and extreme `(k, p)` stays finite.
+- `poisson_pmf(0, 0)` is 1 and the log-space PMFs were probed at their
+  previously-crashing inputs; no remaining overflow class found in the
+  probability module.
+
+## [v2.2.5] - 2026-10-12
+
+### Housekeeping — audit hardening
+
+- Closes the findings of the full-repository audit: patched the concrete
+  defects (correctness, fail-closed behaviour, platform independence),
+  wired every standalone guard into CI, removed dead or duplicated code
+  paths, and pinned every doc claim to a test so it cannot silently
+  drift again. Regression tests fail without the corresponding fix.
+
+## [Unreleased]
+
+### Distribution status of 2.2.2 — read this before assuming npm has it
+
+The two registries are **not** in the same state for 2.2.2.
+
+| Registry | `2.2.2` | Build attestation |
+|---|---|---|
+| **PyPI** `scientific-computing-system` | **published** | **PEP 740 provenance present** |
+| **npm** `scientific-computing-system` | **NOT published** | none — the version does not exist on npm |
+
+PyPI 2.2.2 is live and carries a PEP 740 attestation. Verified against the live
+registries on 2026-10-05: the PEP 740 per-file provenance endpoint returns
+**HTTP 200** for both files.
+
+```
+curl -sS -o /dev/null -w '%{http_code}\n' \
+  https://pypi.org/integrity/scientific-computing-system/2.2.2/scientific_computing_system-2.2.2-py3-none-any.whl/provenance   # 200
+curl -sS -o /dev/null -w '%{http_code}\n' \
+  https://pypi.org/integrity/scientific-computing-system/2.2.2/scientific_computing_system-2.2.2.tar.gz/provenance               # 200
+```
+
+npm 2.2.2 does not exist. The published npm versions remain `1.0.0`, `2.2.0` and
+`2.2.1`. Nothing about the npm launcher is broken — the publish is blocked on a
+one-time npmjs.com registration, described next.
+
+### Pending: register the npm trusted publisher (one-time, maintainer, in a browser)
+
+npmjs.com has **no trusted publisher** configured for the package
+`scientific-computing-system`. Until one exists, the OIDC path cannot complete a
+publish, and npm publishes no provenance for this package.
+
+The coordinates to enter on npmjs.com → package `scientific-computing-system` →
+**Settings → Trusted Publisher → GitHub Actions**:
+
+| Field | Value |
+|---|---|
+| Organization or user | `Furox-Art` |
+| Package | `scientific-computing-system` |
+| Workflow filename | `npm-publish.yml` |
+| Environment name | `npm` |
+| Allowed actions | **`npm publish`** — must be enabled, see the warning below |
+
+**The allowed-actions field is not optional in practice.** npm's current UI grants
+`npm stage publish` by default on newly created configurations and makes direct
+`npm publish` **opt-in**. This repository's workflow calls `npm publish` directly,
+so registering the publisher *without* also allowing `npm publish` will leave the
+publish failing — with a permission error this time rather than a 404.
+
+The same registration from the CLI, using the maintainer's own npm login and 2FA:
+
+```
+npm trust github --file npm-publish.yml \
+  --repo Furox-Art/scientific-computing-system --env npm --allow-publish
+```
+
+### The publish mode default is unchanged, and was never set to token
+
+The mode is the `workflow_dispatch` input `use_token_fallback`, whose default is
+`false` — that is **OIDC**. There is no `npm_publish_mode` variable; the repository
+has **no Actions variables at all** (none at repository or organization scope), and
+`npm_publish_mode` appears nowhere in the tree. Nothing needs to be switched back:
+OIDC is already the default, and token mode remains an explicit per-run opt-in.
+
+`NPM_TOKEN` does still exist as a repository secret. It is what token mode would
+use, and it should be deleted once the trusted publisher is registered and the
+first OIDC publish has succeeded.
+
+### Fixed: a 404 from npm no longer reads as "already published"
+
+`npm publish` answered
+
+```
+npm error 404 The requested resource 'scientific-computing-system@2.2.2' could not
+be found or you do not have permission to access it.
+```
+
+on runs 37268729425 and 37269325567, and that single line cannot distinguish the
+two real causes. npm deliberately does not tell an unauthenticated caller whether a
+package exists, so **an unregistered trusted publisher is reported as 404, not as
+401 or 403.**
+
+Two failure surfaces were making that expensive to diagnose, and both now say so
+out loud. Neither changes what the workflow does; both only change what it prints.
+
+- **The publish step** now names the real cause when npm returns 404, states that
+  the package exists and the version is absent, prints the npmjs.com fields above,
+  and calls out the `npm publish` allowed-action requirement. A rejected or absent
+  token looks different (401, or `ENEEDAUTH`), and the step says that too.
+- **The version-existence gate** now warns, at the point where it would otherwise
+  tell someone to bump the version, that a 404 also means "unauthorized". Bumping
+  to escape a 404 consumes a release number on both registries and still will not
+  publish while the publisher is unregistered.
+
+Worth recording precisely: in **both** runs the version gate **passed**. The
+tarball built, provenance was signed and submitted to the Sigstore transparency
+log, and only the `PUT` failed. So both runs did prove the authentication failure,
+and the fix is the registration above — not a version bump.
+
+## [v2.2.4] - 2026-10-12
+
+### Housekeeping — release alignment
+
+- Publishes the post-2.2.3 repository state (single-shot automatic npm
+  publishing, #165) to PyPI and npm: the 2.2.3 upload predates that commit, so
+  both registries were one commit behind `main`. No behavioural change.
+
+## [v2.2.3] - 2026-10-05
+
+This release exists to exercise the OIDC trusted-publish path, now that the
+npmjs.com trusted publisher for `scientific-computing-system` is registered.
+
+The previous npm 2.2.2 was published in token mode and therefore carries no
+attestation. Nothing about the launcher changed: `src/` is untouched since
+2.2.2, and the only source change in this release is the version string itself.
+
+## [v2.2.2] - 2026-10-05
+
+Clears the last 17 open CodeQL alerts in this repository. None of them was a
+security vulnerability, and **none was a logic defect** — no discarded result, no
+missing `return`. Nothing is suppressed: there is no `# nosec`, no path exclusion
+and no `codeql.config` entry.
+
+### Behaviour change
+
+**One, and it is a removal:** the private path `cds.cli._parser._build_parser` no
+longer resolves.
+
+`_build_parser` was an alias for `build_parser`, kept for backwards
+compatibility. It was defined in `cds.cli._parser` but imported and re-exported by
+`cds.cli.__init__`, so within its own module it was genuinely unreferenced —
+which is exactly what `py/unused-global-variable` reported. The assignment has
+moved to `cds.cli.__init__`, beside its only consumer and inside the `__all__`
+that already exports it.
+
+- `cds.cli._build_parser` is unchanged: still present, still in `__all__`, still
+  the same object as `cds.cli.build_parser`. This is the documented
+  backwards-compatibility surface and it keeps working.
+- `cds.cli._parser._build_parser` is gone. Nothing in this repository referenced
+  it and the name is underscore-private, but a downstream script that reached
+  into the private submodule would break.
+
+There is now a test pinning the alias, because the original defect was that
+nothing asserted it existed.
+
+### Fixed
+
+- **Protocol placeholders are docstrings, not bare `...`.** Nine
+  `py/ineffectual-statement` alerts across `src/cds/ml/model_selection.py`,
+  `src/cds/ml/voting.py` and `src/cds/tools/adapters.py` were the conventional
+  `...` terminating a `typing.Protocol` method. These are false positives in the
+  strict sense: `...` is the documented placeholder for a structurally-typed
+  method whose implementation lives in the real backend module, and no code path
+  executes it. `SoftVotingModel` is the only `@runtime_checkable` one, and
+  `isinstance` against a runtime protocol inspects attribute *presence* without
+  calling the body.
+
+  They became docstrings rather than `pass` because coverage.py excludes an
+  ellipsis-only body but counts `pass`; measured, swapping it in drops those
+  lines from 100% to 75% and breaks the coverage gate. `raise NotImplementedError`
+  has the same coverage problem and would additionally change behaviour if the
+  body were ever reached. `src/cds` already contained nine docstring-only bodies
+  with no alert on any of them.
+
+- **`src/cds/tools/registry.py` imports `importlib` one way.** Three spellings
+  were mixed: `import importlib`, `import importlib.util` and
+  `from importlib import metadata`. The first was fully subsumed by the second.
+  Now `import importlib.metadata` and `import importlib.util`, with call sites
+  fully qualified. Four monkeypatch targets in `tests/` were retargeted to match.
+
+- **Four `py/unnecessary-lambda` alerts in the test suite.** `lambda x: max(x)`
+  and `lambda values: sum(values)` are plain wrappers around a callable; the
+  callables are now passed directly.
+
+- **`tests/test_fitting_bootstrap.py` imports `cds.modeling.fitting` one way.**
+  A module-level `from ... import` coexisted with function-local
+  `import ... as fitting`. The single `import ... as fitting` form is used now and
+  the module-level names are qualified through it.
+
+### Added
+
+- **`tests/test_protocol_placeholders.py`** pins the protocol bodies on the AST,
+  because a docstring-only body and a docstring followed by `pass` compile to
+  almost identical instructions and only the syntax tree tells them apart. It also
+  asserts the placeholder semantics (`None` when called unbound), that
+  `SoftVotingModel` is still a working structural contract, and that every
+  declared signature and annotation still resolves. Negative-controlled against
+  four mutations, all caught: docstring-plus-`pass`, `...` reinstated, body
+  replaced by a real statement, and a statement appended after the docstring.
+
+### Changed
+
+- README's pasted `cds --version` transcript now reads `System version 2.2.2`.
+  Every provenance and attestation statement in `README.md` and `SECURITY.md`
+  still refers to **2.2.1** deliberately: those describe the published release,
+  including its digests, and remain true until a newer one ships.
+
+
+### Fixed
+
+- **Provenance claims are now scoped, measured, and guarded.** A follow-up report
+  asserted that PyPI had no PEP 740 attestation either. Re-measured directly, that
+  is **not** the case, so the previous text was left standing and made precise
+  rather than weakened:
+
+  - PyPI **2.2.1** serves a PEP 740 provenance bundle for **both** the wheel and
+    the sdist (HTTP 200 on the per-file `/integrity/.../provenance` endpoint),
+    and each bundle's `subject` digest equals the `sha256` PyPI publishes for
+    that file. The 404 in the report came from requesting
+    `https://pypi.org/integrity/scientific-computing-system/2.2.1/`, which is a
+    directory, not the per-file endpoint.
+  - npm **2.2.1** has **no** attestation: the attestations endpoint returns 404.
+    This part of the report was correct.
+
+  The security posture is therefore unchanged and more precisely stated. What
+  changed: `SECURITY.md` now separates the three things that were being conflated
+  — a **PEP 740 attestation** (Sigstore-signed, attests *who built this*),
+  **npm `dist.signatures`** (registry transport signing, attests nothing about
+  the build), and a **content digest** (`sha256` on PyPI, `dist.integrity` on
+  npm; pins *which bytes*, not *where they came from*). It lists the published
+  digests to pin, gives the commands that verify them, and states the exact
+  trusted-publisher coordinates still to be registered for npm.
+
+- **Reproducible-build claim scoped to what was actually measured.** Two
+  consecutive builds of the same commit with the same pinned backend produced
+  byte-identical wheel and sdist. Those digests do **not** match the published
+  ones (the release runs a hash-locked Linux toolchain; the check ran elsewhere),
+  so the documentation now claims determinism for a fixed toolchain and
+  explicitly declines to claim the published artifacts are bit-for-bit
+  reproducible from source.
+
+- **npm launcher prerequisite re-verified.** With `cds` absent from `PATH`, the
+  shim proceeds straight to interpreter resolution (`python`/`python3`/`py`) and
+  runs `python -m cds`; it never looks for a `cds` console script. README,
+  `SECURITY.md` and the docs already agreed on this wording, and it is now
+  backed by an explicit check rather than by reading the source.
+
+### Added
+
+- `docs/checks/verify_provenance_claims.py` — a guard that parses the attestation
+  claims out of `README.md` and `SECURITY.md` and compares them against the live
+  registries, failing if the prose asserts something the registries contradict.
+  It also rejects prose that overstates `dist.integrity` as provenance or allows
+  the attested subject to differ from the published digest. Negative-controlled:
+  three false claims (PyPI not attested, npm attested, digest mismatch acceptable)
+  each turn it red. Wiring it into CI is left to the workflow owner; this change
+  is docs-only by scope.
+
+## [v2.2.1] - 2026-10-04
+
+Documentation and release-surface corrections. **No library behaviour change**:
+nothing under `src/cds/` was modified except the `__version__` constant, so no
+numerical kernel, public API signature or CLI subcommand differs from 2.2.0.
+
+The reason this patch release exists: `README.md` is the `long_description`, and
+PyPI only re-reads it when a new release is uploaded. 2.2.0 shipped the README as
+it stood before the truthfulness work below, so the PyPI project page for 2.2.0
+still advertises claims the repository has since retracted. Publishing 2.2.1 is
+what makes the corrected README the one PyPI renders.
+
+### Fixed
+
+- **README performance claim corrected to the committed artifact.** The "catch"
+  paragraph asserted "~0.05 s versus ~0.0001 s ... roughly 580x slower" and
+  described it as "this machine's benchmark run", while pointing readers at
+  `docs/benchmarks.md` for "the hardware they came from". `benchmarks/results.json`
+  actually records 0.0696 s versus 0.000060 s (**1154.8x**) at commit `7213425`,
+  and that same file records Platform / CPU / Python / NumPy as "not recorded"
+  with an explicit "treat the absolute timings as unverified" warning. The line
+  added by the earlier truthfulness commit therefore contradicted the warnings it
+  shipped alongside. Both the README and `docs/why-pure-python.md` now quote the
+  artifact's own numbers and state that the environment was not recorded.
+
+- **npm launcher prerequisite stated correctly.** README and `SECURITY.md` said
+  the `scs` shim works once `cds` is "on your PATH". `index.js` resolves an
+  interpreter (`python`/`python3`/`py`) and runs `python -m cds`; it never looks
+  for a console script on `PATH`. Corrected to "requires the Python distribution
+  installed so that `python -m cds` resolves".
+
+- **Stale version references left behind by the 2.2.1 bump.** The README's pasted
+  `cds --version` transcript still read `System version 2.2.0` after the version
+  moved, and `SECURITY.md` still recommended pinning `==2.2.0`. Since the README
+  is the `long_description`, that line would have shipped verbatim to the PyPI
+  project page. Both were re-derived from live commands at 2.2.1.
+
+  Every other pasted transcript was re-checked against the installed 2.2.1 wheel
+  and found current: the quickstart output (SVD singular values, damped-oscillator
+  final state, regression fit), `cds modules` printing 26 rows and omitting exactly
+  the nine documented modules, the structural claims (34 subpackages, 35 public
+  feature modules, 505 names / 342 functions / 163 classes), the benchmark ratio
+  against `benchmarks/results.json`, and all five documented extras.
+
+  Two further `SECURITY.md` claims were false and are corrected: `scs` was
+  documented as needing a `cds` console script on `PATH` when the launcher
+  resolves an interpreter and runs `python -m cds` (verified: the shim prints
+  `System version 2.2.1` with no `cds` on `PATH`), and the PyPI attestation cell
+  claimed a PEP 740 bundle for the published 2.2.0 when PyPI serves none.
+
+  The pin example is now version-agnostic by construction, so it cannot rot at
+  the next bump.
+
+- **Module-surface claims are now accurate.** "34 subpackages" silently omitted
+  the two top-level public modules (`causal.py`, `sensitivity.py`), and
+  "`cds modules` for the live list" was wrong twice over: that command prints a
+  curated 26-entry subset and omits `bayes`, `causal`, `core`, `fractals`,
+  `genetics`, `infotheory`, `interpolate`, `pde`, and `wavelets`. README,
+  `docs/api.md` and `docs/index.md` now state the real counts and flag
+  `cds modules` as a subset. The unsupported "46 public functions / 534 exports"
+  hero claim does not exist in the repository or in any reachable commit; the
+  README instead carries counts derived from the package itself (505 exports:
+  342 functions, 163 classes across 35 feature modules).
+
+- **Documentation no longer claims npm is unpublished.** npm 2.2.0 is live and
+  npm is a supported channel, but `README.md` line 41 still said "npm is no
+  longer published". Because `README.md` is listed in the npm `files` allowlist,
+  that sentence shipped **verbatim inside the published 2.2.0 tarball**, so the
+  npm package page contradicted its own README. `README.md`, `SECURITY.md` and
+  `docs/related.md` now describe both channels accurately; the npm version badge
+  is restored now that the registry and PyPI agree.
+
+- **A successful publish is no longer reported as a failure while npm is still
+  propagating it.** `npm publish` returns as soon as the registry accepts the
+  upload, but the version becomes readable on the read path asynchronously. The
+  post-publish check read once, immediately, and on run `37136131220` got
+  `npm error 404 No match found for version 2.2.0` — while 2.2.0 was in fact
+  published and recorded by the registry ninety seconds later. A maintainer
+  reading that run had every reason to believe the release had broken. Three
+  sibling repositories hit the same false failure.
+
+  The check now polls the registry with backoff over a budget of several minutes,
+  succeeds on the first match, and still fails closed if the version genuinely
+  never appears, emitting a `::warning::` first so a slow-but-successful publish
+  is never read as a hard failure.
+
+  It queries the registry's JSON API instead of `npm view`, which was a poor fit:
+  it reports "absent" and "denied" with the same `E404`, and it resolves against
+  the userconfig the job created for *writing*, so a read-only confirmation had no
+  reason to touch publish credentials at all. Both directions are exercised
+  against a stub registry, and the retry budget itself is asserted, since
+  shortening it to make a test fast is what caused the bug.
+
+- **The publish path is now guarded rather than merely enabled.** The launcher
+  contract test previously asserted that publishing stayed disabled, which would
+  have silently passed against a disabled workflow. It now asserts a real
+  `npm publish --provenance` invocation, `id-token: write`, the absence of
+  `private: true`, the absence of the disabled stub, and the presence of every
+  gate that makes a publish safe: the registry version-existence check, the
+  `npm pack --dry-run` tarball allowlist, and the npm/Python version lockstep.
+
+- **The npm toolchain version floor rejected a compliant toolchain.** The first
+  real publish run failed on this gate:
+
+  ```
+  npm --version | grep -Eq '^11\.(5[1-9]|[6-9][0-9])\.|^1[2-9]\.'
+  ::error::npm 11.5.1+ is required for OIDC trusted publishing
+  ```
+
+  On Node 24, setup-node installs npm **11.19.0**. The `[6-9][0-9]` alternative
+  covers minors 60-99, so `19` never matched and the gate failed on a toolchain
+  that meets the floor. A regex cannot express "greater than or equal to" for a
+  dotted version without enumerating every minor, which is exactly the mistake
+  that shipped. The gate now parses the version, strips any leading `v` and
+  prerelease suffix, and compares major/minor/patch as integers against 11.5.1.
+  The Node half of the same gate ignored the patch component: it compared only
+  major and minor, so `22.9.0` was accepted even though the documented floor is
+  22.14.0. Both halves now use the same integer comparison.
+
+- **Token-mode npm publish failed with `ENEEDAUTH` while holding a valid
+  secret.** The run reached `npm publish` with `NODE_AUTH_TOKEN` populated and
+  still got:
+
+  ```
+  npm error code ENEEDAUTH
+  npm error need auth This command requires you to be logged in to
+                        https://registry.npmjs.org/
+  ```
+
+  Root cause: `actions/setup-node` was configured without `registry-url`, so it
+  wrote no npm userconfig at all. `NODE_AUTH_TOKEN` on its own is inert — npm only
+  substitutes it into a credential when some userconfig maps
+  `//registry.npmjs.org/` to `${NODE_AUTH_TOKEN}`. With no such entry npm never
+  attempts authentication, which is why the failure was `ENEEDAUTH` (no
+  authentication attempted) rather than `E401` (attempted and rejected) even
+  though the secret was present and correct. The fix is
+  `registry-url: "https://registry.npmjs.org"` on `setup-node`.
+
+  Separately, the credential check lived inline inside the publish step, so its
+  failure text appeared in the log while `npm publish` was invoked anyway. It is
+  now its own step ahead of both publish steps, so a non-zero exit ends the job
+  before npm can run, and it covers the OIDC mode too (verifying the runner
+  actually granted `id-token: write`, which the previous version never checked).
+
+- **The `bin` map is now pinned by tests, so a broken launcher command cannot
+  ship silently.** The `npm warn publish "bin[scs]" script name bin/scs.js was
+  invalid and removed` message had been reported as a defect that would leave
+  the published package with no working `scs` command. **That report was wrong.**
+  npm normalises the redundant `./` prefix and ships the entry either way; the
+  packed tarball keeps `bin: { scs: "./bin/scs.js" }` alongside `bin/scs.js`, and
+  installing it creates `scs`, `scs.cmd` and `scs.ps1` and `scs --version`
+  succeeds. `axiomize@1.12.4`, published from the identical shape, ships the same
+  and is not deprecated. No `package.json` change is required.
+
+  What *is* a real hazard is the opposite: npm ships a `bin` pointing at a
+  missing file, or one excluded by `files`, with **no warning at all**. Five
+  tests now assert the bin map is a valid command-name to path mapping, that
+  every target exists and is covered by `files`, that the shim carries a `node`
+  shebang, and that the real tarball (`npm pack --dry-run --json`) still contains
+  both the shim and the bin entry. One further test documents that the `./`
+  prefix is intentional so the cosmetic warning is not "fixed" by a future
+  maintainer.
+
+### Added
+
+- **`tests/test_readme_surface.py`** derives the README's structural claims from
+  `src/cds/` and from the installed package: subpackage count, presence of both
+  top-level public modules, the export total, per-module table coverage, the
+  benchmark ratio against `benchmarks/results.json`, and a guard against
+  describing `cds modules` as exhaustive. This drift was previously invisible to
+  CI, which is how it survived several releases. Verified by mutation: five
+  separate re-introductions of the audited defects each turn the suite red.
+
+- **`codemeta.json` is now a locked version surface.** It was left out of the
+  original five surfaces and drifted: it still declared `2.1.0` after the package
+  reached 2.2.0, while every other surface had moved. CodeMeta is a
+  machine-readable publication record, so a stale `version` there advertises the
+  previous release to every automated consumer while the installed package
+  reports a different one. `scripts/check_version_lockstep.py` now reads it and
+  `tests/test_codemeta_version_lockstep.py` fails CI on drift. It is also added
+  to the sdist allowlist, without which that suite failed with `FileNotFoundError`
+  when run from an unpacked sdist.
+
+- README coverage: `cds.core` and `cds.graph` rows, `examples/` (35 runnable
+  files) and `dashboard/app.py` entries, all 13 CLI subcommands, the `[pandas]`
+  extra, `paper.md`/`paper.bib` (JOSS) and `codemeta.json`, and a Contributing
+  section with the `pip install -e ".[dev]"` / `pytest` / `mkdocs serve` loop and
+  the 100% blended-coverage gate. Duplicated prose was removed (the supply-chain
+  section now defers to `SECURITY.md` instead of restating it, and the generic
+  "Common use cases" filler is gone).
+
+- **Two supported npm publish modes**, selected by the `use_token_fallback`
+  dispatch input (boolean, default `false`):
+  - **OIDC trusted publishing** (preferred, default) — `id-token: write`,
+    `npm publish --provenance`. No registry secret involved.
+  - **Token mode** (`use_token_fallback=true`) — uses the repository's existing
+    `NPM_TOKEN` secret via `NODE_AUTH_TOKEN`. This is the mode in use while the
+    npmjs.com trusted-publisher registration is pending.
+
+  The token mode deliberately omits `--provenance`. Provenance is an OIDC-only
+  Sigstore attestation: a token cannot mint one, and npm rejects the
+  combination. The token mode prints a NOTICE that the release carries no
+  provenance rather than passing a flag that cannot work or implying an
+  attestation exists. Both modes are fail-closed: a requested mode with no usable
+  credential exits non-zero with an actionable message, and token mode never runs
+  automatically, so a broken OIDC configuration cannot silently downgrade to the
+  long-lived credential.
+
+### Changed
+
+- **npm publishing is real again.** This reverses two earlier decisions, both
+  deliberate at the time and recorded here so the history is not silently erased:
+  the decision in `52717c5` to disable npm publishing (which replaced the publish
+  step with `run: echo "npm publishing is disabled; PyPI is the install path" &&
+  exit 0`), and `"private": true` in `package.json`, added by `#140` while
+  publishing was disabled. `private: true` makes `npm publish` refuse to run at
+  all, so the flag had to go before the workflow could work. The `files` allowlist
+  is retained: it is what keeps the repository (tests, CI workflows, 10k+
+  statements of Python, promo media) out of the published tarball. The npm
+  channel is on OIDC trusted publishing (`id-token: write`,
+  `npm publish --provenance`); no long-lived registry token is used on the
+  primary path.
+
+- README shortened with **higher** coverage: the supply-chain section dropped from
+  209 lines to a 3-line summary plus a link, and "The catch" reduced to a short
+  paragraph.
+
+- **This release carries a PyPI attestation; 2.2.0 does not.** PyPI's JSON API
+  reports zero PEP 740 attestation bundles for 2.2.0, which went out in token
+  mode — a token cannot mint a Sigstore attestation. 2.2.1 is published by
+  `release.yml` through `pypa/gh-action-pypi-publish` with Trusted Publishing
+  (OIDC), so it will carry one, as long as the `pypi` environment's trusted
+  publisher is configured — a misconfiguration fails the publish loudly rather
+  than degrading silently.
+
+## [v2.2.0]
+
+Security hardening of the provenance path surface: provenance manifest paths
+are confined (`src/cds/_paths.py`), and the runtime dependency graph is guarded.
+No numerical kernel or public API signature changed. (Content owned by the
+security agent; this heading exists to satisfy the version-lockstep gate.)
+
+## [v2.1.0] - 2026-09-30
+
+Release-hardening pass covering the CI, quality-gate and packaging surface. No
+numerical kernel, public API signature or `cds` CLI subcommand changed.
+
+New public modules that first shipped in this release line (noted here because
+the release notes below cover only the hardening pass): `cds.validation`
+(cross-method verification, distribution-shift reporting), `cds.causal`
+(assumption-gated estimators — no causal-structure inference from observational
+correlation), `cds.sensitivity` (local and variance-based global sensitivity,
+identifiability), `cds.units` (SI dimensional analysis), `cds.workflow`
+(approval-gated, fail-closed orchestration), `cds.provenance` (manifests,
+hashing, checkpoints), `cds.data_io` (streaming I/O, optional HDF5/NetCDF),
+`cds.tools` (lazy optional-backend adapters), and `cds.uncertainty` (analytic
+and correlated Monte-Carlo propagation).
+
+### Fixed
+
+- **npm launcher (`index.js`, `bin/scs.js`)**: the published launcher could not be
+  parsed by Node (`SyntaxError: Unexpected token ';'`), and had it parsed it
+  spawned `python -m scs.cli`, a module that has never existed in any release
+  (the import name is `cds`). Both defects shipped in `1.0.0` on npm and were
+  invisible because `npm test` was a placeholder that exited 1 without running
+  anything. The launcher is now syntactically valid, targets `python -m cds`,
+  propagates the child's exit status, and reports one actionable message when no
+  interpreter is found.
+- **npm package contents**: `package.json` shipped no `files` allowlist, so a
+  publish would have uploaded the whole repository (tests, workflows, 10k+
+  statements of Python, promo media). Publication is now restricted to an
+  explicit allowlist.
+- **npm version drift**: `package.json` declared `1.0.0` while the Python
+  distribution was at `2.1.0`. It now tracks the Python version and CI fails on
+  any drift.
+- **Version-discipline bypass under rebase merges**
+  (`scripts/check_version_discipline.py --base-ref HEAD^1`): `HEAD^1` resolves to
+  the previous commit of the *same branch*, so in a multi-commit rebase merge only
+  the final commit's diff was inspected. A PR could change `src/cds/` in one
+  commit, follow with an unrelated commit, and pass the gate with no version bump
+  at all. The gate now diffs against the PR merge-base.
+- **Release fail-closed behaviour**: the publish job could report success after a
+  verification step had failed. That path is closed; every verification failure
+  now fails the job before any registry or tag mutation.
+- **Docs deployment ordering**: `deploy-docs` depended only on the `test` matrix,
+  so gh-pages could be updated from a run whose `audit`, `version_discipline` or
+  `test`-aggregate gates had failed. It now depends on the aggregate `CI` job.
+- **sdist test-suite failure**: `tests/test_release_contract.py` reads
+  `.github/workflows/*.yml`, which the sdist `only-include` list omitted, so the
+  shipped source distribution could not pass its own test suite (13 failures).
+  The CI workflow files are now part of the sdist.
+
+### Added
+
+- **`npm test` contract suite** (`npm.test.js`): assertions covering
+  `node --check` parseability, the `cds` module target, argument forwarding, exit
+  status propagation, the `files` allowlist, npm/Python version agreement, and a
+  guard that `npm-publish.yml` stays a disabled no-op. CI runs `npm run check`
+  and `npm test` on every push and pull request; **nothing in CI publishes to
+  a registry**.
+- **`scripts/check_version_lockstep.py`**: machine-enforced agreement across
+  `pyproject.toml`, `package.json`, `src/cds/_version.py`, `CITATION.cff`, the
+  runtime `cds.__version__` import, `CHANGELOG.md` and -- with `--dist-dir` --
+  the built wheel and sdist metadata. `2.1.0` had shipped to PyPI with no
+  `CHANGELOG.md` entry; that class of drift is now a red build.
+- **Wheel/sdist content assertions in CI**: the packaging job now asserts the
+  exact filename, distribution name, version, `py.typed` marker, sdist root
+  directory and the absence of forbidden paths (test fixtures, promo media,
+  `.github`, `site/`) rather than building artifacts and trusting them.
+- **Timeouts on every CI job** and per-job least-privilege `permissions:`.
+
+### Changed
+
+- All GitHub Actions references are pinned to full immutable commit SHAs;
+  previously several workflows used mutable `@v4` / `@v7` / `@v8` tags.
+- Branch ruleset for `main` extended in place (not replaced) to require the
+  aggregate `CI` check plus the `Installed CLI Smoke`, version-discipline,
+  packaging and npm contract jobs, and to dismiss stale reviews on push.
+- npm publishing stays disabled per product decision ("npm is no longer
+  published"; `npm-publish.yml` is a deliberate no-op). `package.json` is marked
+  `private`, the npm contract test asserts the workflow stays a no-op, and
+  nothing in CI uploads to a registry.
+- Removed the dead workflow files that main did not already remove:
+  `wsl-science-runner-smoke.yml` (targeted a self-hosted runner label with zero
+  registered runners). The retired `public-external-validation-p08-*` experiment
+  workflows and the one-shot `p08-cancel-noncanonical-runs.yml` /
+  `tmp-compassion-raw-acquire.yml` jobs were deleted on `main` directly and are
+  kept deleted here.
+
+## [v2.0.1] - 2026-09-29
+
+Metadata-only patch release for improved PyPI discoverability. No runtime API or numerical behavior changes.
+
+### Changed
+
+- Expanded PyPI keywords and classifiers for reproducibility, uncertainty quantification, sensitivity analysis, dimensional analysis, scientific workflows, ODE/PDE, and related scientific-computing searches.
+- Refreshed development lock versions required by the current security audit.
+- Normalized repository trailing whitespace required by pre-commit.
+
+
+### Added
+
+- **Random Forest classifier** (`cds.ml`): bagged CART trees with
+  bootstrap resampling and per-split feature randomization (`sqrt`/`log2`
+  / explicit count), fully deterministic under a seed.
+- **Metrics** (`cds.ml`): `accuracy`, `confusion_matrix`,
+  `precision_recall_f1`, `macro_prf`, regression `mse`/`mae`/`r2_score`,
+  and tie-aware rank-based `roc_auc`.
+- **Cross-validation** (`cds.ml.model_selection`): `k_fold_indices` and
+  `cross_val_score` over the shared estimator interface.
+- **Interpolation module** (`cds.interpolate`): `interp1d` (linear /
+  nearest) and `interp2d` (bilinear on regular grids).
+- **SVD** (`cds.math_utils`): one-sided Jacobi decomposition with
+  `svd`, `rank` and `condition_number`; full U/Vt factors.
+- **STFT / spectrogram** (`cds.signals`): Hann/Hamming windows, framed
+  zero-padded transforms reusing the radix-2 FFT, `STFTResult`.
+- **Gradient Boosting classifier** (`cds.ml`): logistic-loss boosted
+  regression trees with Newton leaf values; binary labels.
+- **Bootstrap confidence intervals** (`cds.stats`): percentile-method
+  `bootstrap_ci` and two-sample `bootstrap_diff_ci`.
+- **Metropolis-Hastings sampler** (`cds.montecarlo`): 1-D random-walk
+  MCMC with burn-in/thinning and acceptance-rate reporting.
+- **Symplectic integrators** (`cds.diffeq`): semi-implicit Euler and
+  velocity Verlet with forward/backward integration.
+- **Constrained optimization** (`cds.optimization`): projected gradient
+  descent for box bounds and quadratic-penalty constrained solves.
+- **Hypergeometric & negative-binomial distributions**
+  (`cds.probability`), pmf + cdf for both.
+- **TF-IDF ranked retrieval** (`cds.knowledge`): `rank_tfidf` across
+  concepts and notes with smoothed idf.
+- **Haar wavelet transform** (`cds.signals`): `dwt` / `idwt` /
+  `dwt_multi_level`, orthonormal with perfect reconstruction.
+- **PDE solvers** (`cds.pde`): explicit FTCS heat equation (Dirichlet /
+  Neumann, stability-guarded) and wave equation (CFL-guarded).
+- **Gaussian Naive Bayes** (`cds.ml`): log-space scoring with variance
+  smoothing.
+- **Correlation-mining engine** (`cds.hypothesis`): `mine_correlations`
+  turns numeric datasets into statistically tested, falsifiable
+  `Hypothesis` objects.
+- **Power analysis** (`cds.stats`): `power_t_test`,
+  `power_proportion_test` and `required_n_per_group` sample-size solver.
+- **VotingClassifier** (`cds.ml`): hard (majority vote) and soft
+  (averaged probabilities) ensembles over the shared estimator interface.
+- Four new runnable demos under `examples/`: interpolation, PDE,
+  ensemble showcase and the end-to-end discovery pipeline.
+- **PCA end-to-end demo** (`examples/pca_demo.py`): scaling vs raw
+  variance comparison, component selection, 2-D ASCII projection,
+  reconstruction error and train/test discipline, with a matching
+  tutorial (`docs/tutorials/pca_demo.md`).
+- **ML correctness reference table** (`scripts/verify_ml_reference.py`,
+  `docs/ml_reference.md`), LogisticRegression, DecisionTree, KMeans,
+  PCA and LinearRegression checked against scikit-learn 1.9.0 outputs
+  on a fixed seeded dataset; one-command, dependency-free verification.
+
+### Changed
+
+- `DecisionTreeClassifier` now accepts `max_features` and `seed` for
+  random-forest-style split randomization (default behavior unchanged).
+- The README now displays the sklearn-parity badge and links the ML
+  Reference table. (The matching `ml-reference` CI job is prepared but
+  not yet applied. It needs a push from a token with the `workflow`
+  OAuth scope; see the `backup/pre-reorder` branch.)
+
+## [v2.0.0] - 2026-09-05
+
+Scientific workflow platform release. Reorganises the project from a numerical
+methods library into a layered system that separates computation, analysis,
+scientific assurance, orchestration, and data handling.
+
+### Added
+
+- Uncertainty propagation, provenance capture, and tool discovery.
+- Dimensional analysis, domain checks, and scalable data I/O.
+- Scientific adapters, sensitivity analysis, and tool orchestration.
+- CLI catalog refreshed for the expanded module set.
+
+### Changed
+
+- The project is organised into explicit layers (compute / analysis /
+  assurance / orchestration / data) with dependencies pointing downward.
+- Release pipeline enforces a single publish authority.
+
+## [v1.6.2] - 2026-08-23
+
+Patch release carrying the PyPI deprecation tombstone for the former
+`cognitive-discovery-system` distribution name, pointing users at
+`scientific-computing-system`. No API change; the import name stayed `cds`.
+
+## [v1.6.1] - 2026-08-21
+
+A **patch** release completing the JSON round trip for core data models.
+
+### Added
+
+- **`cds.core`**: `Hypothesis.from_dict()`: the inverse of `to_dict()`.
+  CLI/JSON output can now be re-imported: enum strings are coerced back to
+  `Domain` / `HypothesisStatus`, ISO-8601 timestamps are parsed, and missing
+  optional keys fall back to constructor defaults. Invalid `status` values
+  raise `ValueError`.
+
+### Changed
+
+- Internal layering cleanup: shared special-function kernels moved to their
+  single home (`cds.math_utils.special`) so lower-level packages never depend
+  on higher-level ones; a suite-level import-direction guard enforces this.
+- `cds.cli` is now a package (`_style` / `_handlers` / `_parser`) with
+  identical behaviour; refreshed module descriptions in `cds modules`.
+
+## [v1.6.0] - 2026-08-21
+
+A **minor** release deepening the ML, probability, ODE, and optimization
+toolkits toward scikit-learn / SciPy teaching parity, still zero runtime
+dependencies, still 100% blended coverage.
+
+### Added
+
+- **`cds.ml`**: `KNeighborsClassifier` / `KNeighborsRegressor` (brute-force,
+  deterministic tie-breaking), `KMeans` (k-means++ seeding, seeded),
+  `DecisionTreeClassifier` (CART + Gini), `LogisticRegression` (stable-BCE
+  gradient descent, optional L2), `LinearRegression` (closed-form vector OLS
+  via normal equations), `PCA` (cyclic Jacobi eigen-solver, transform /
+  inverse_transform), `StandardScaler`, `train_test_split` (seeded)
+- **`cds.probability`**: chi-square and Student-t distributions
+  (`chi2_pdf/cdf/ppf`, `t_pdf/cdf/ppf`), `gamma_pdf` + `sample_gamma`
+  (Marsaglia–Tsang with shape<1 boost), `beta_pdf` + `sample_beta`
+  (exact gamma-ratio identity)
+- **`cds.diffeq`**: implicit stiff solvers: `backward_euler`,
+  `trapezoid_method` (Crank–Nicolson) and their `_system` variants; unified
+  θ-method core with Newton iteration over analytic or central-difference
+  Jacobians via the shared PLU solver
+- **`cds.optimization`**: `nelder_mead` simplex (degenerate-simplex and
+  symmetric false-convergence guards), `simulated_annealing` (Metropolis rule,
+  box bounds, seeded)
+- **`cds.stats`**: nonparametric tests: `mann_whitney_u` and
+  `wilcoxon_signed_rank` with tie/zero corrections (normal approximation)
+
+### Fixed
+
+- Test-suite pyplot figures are now closed per test, silencing matplotlib's
+  "more than 20 figures" memory warning in long sessions
+
+### Changed
+
+- README "Why CDS?" pitch strengthened with proof numbers and a cross-domain
+  snippet; stale counts/versions synced across metadata (19 modules)
+
+## [v1.5.0] - 2026-07-20
+
+A **minor** release expanding algorithms across graph theory, Monte Carlo,
+linear algebra, and CLI, still zero runtime dependencies.
+
+### Added
+
+- **`cds.graph`**: `degree`, `connected_components`, `bellman_ford`,
+  `floyd_warshall`, `prim_mst`
+- **`cds.montecarlo`**: `mc_expectation`, `hit_or_miss` (2-D area estimation)
+- **`cds.math_utils`**: `vector_norm`, `frobenius_norm`, `matrix_trace`
+- **CLI**: `cds integrate <sin|cos|exp|x2|unit> --a --b -n --method`
+
+## [v1.4.0] - 2026-07-20
+
+A **minor** release expanding core scientific APIs and CLI ergonomics.
+Zero runtime dependencies preserved.
+
+### Added
+
+- **`cds.probability`**: CDFs (`gaussian_cdf`, `uniform_cdf`, `exponential_cdf`),
+  `geometric_pmf`, samplers (`gaussian_sample` Box–Muller, `exponential_sample`,
+  `poisson_sample` Knuth)
+- **`cds.stats`**: `spearman_correlation` (midranks), `percentile`, `z_scores`
+- **`cds.scientific`**: constants `epsilon_0`, `g`, `mu_0`; formulas
+  `coulomb_force`, `centripetal_acceleration`, `pendulum_period`, `doppler_frequency`
+- **CLI**: `cds stats <nums>`, `cds sample <dist> -n N --seed …`
+
+### Changed
+
+- `cds info` no longer hardcodes a stale test count; module list includes modeling/knowledge/nlp
+
+## [v1.3.2] - 2026-07-20
+
+A **patch** release expanding the optional ``cds[plot]`` surface.
+
+### Added
+
+- **`cds.plot` charts**: `plot_multi_series`, `plot_scatter`, `plot_regression`
+  (OLS via `cds.stats`), `plot_power_spectrum` (via `cds.signals`),
+  `plot_seasonal_decompose` (4-panel), `plot_heatmap`, `plot_loss`,
+  `save_figure(..., close=)` helper; histogram gains ``density=``
+- **CLI**: `cds plot … --kind series|hist|acf --file out.png`
+
+### Changed
+
+- Docs / Cookbook / demo updated for the expanded plot API
+
+## [v1.3.1] - 2026-07-20
+
+A **patch** release. Fixes the console entry point so `cds` works after a
+plain PyPI install.
+
+### Fixed
+
+- **`[project.scripts]`**: entry point was `cds.cli:app` but the CLI exports
+  `main` (argparse). Installing from PyPI then raised
+  `ImportError: cannot import name 'app' from 'cds.cli'`. Now points to
+  `cds.cli:main`. `python -m cds` was already correct.
+
+## [v1.3.0] - 2026-07-20
+
+A **minor** release focused on **visualization and ergonomics**. Adds the
+optional ``cds[plot]`` matplotlib extra, a CLI PNG export path, a companion
+notebook, and documentation. The zero-dependency core is unchanged: matplotlib
+is only imported when a plot function runs (or when ``cds plot --file`` is
+used).
+
+### Added
+
+- **`cds.plot` optional package** (`src/cds/plot/`):
+  - `plot_series`, `plot_histogram`, `plot_waveform`, `plot_spectrum`
+  - `plot_acf` / PACF stems via `cds.stats` time-series helpers
+  - `plot_optimization_path` for 2-D optimizer trajectories
+  - Lazy matplotlib backend with install-hint `ImportError`
+- **Extra**: `pip install scientific-computing-system[plot]` (also in `[all]`)
+- **CLI**: `cds plot 1,2,3 --file out.png` saves a PNG when matplotlib is
+  installed; without `--file` the existing ASCII terminal plot remains
+- **Examples**: `examples/plot_demo.py`, `examples/plotting_notebook.ipynb`
+- **Docs**: Cookbook matplotlib section, API reference for `cds.plot`, README /
+  module tables, ROADMAP v1.3.0 track
+
+### Changed
+
+- CI main matrix installs `.[pandas,plot]` so optional bridges stay at 100%
+  coverage; minimal-deps job omits `cds/plot/*` like `pandas_io`
+- PyPI description mentions optional matplotlib plotting
+
+## [v1.2.3] - 2026-06-29
+
+A **patch** release. Fixes the release pipeline that silently broke every
+publish since v1.1.8.
+
+### Fixed
+
+- **Release workflow (`release.yml`)**: removed an invalid
+  `administration: write` entry from the `sync-about` job's `permissions:`
+  block. `administration` is not a valid `permissions:` key, so GitHub
+  rejected the entire workflow file as a "workflow file issue" before any
+  job could start, failing in 0s and leaving v1.1.9 onward without a PyPI
+  upload or GitHub Release. The About-sync step is now best-effort
+  (`continue-on-error: true`) since `gh repo edit` needs an admin REST
+  scope the default `GITHUB_TOKEN` can't grant; the repo description is
+  synced by hand on release.
+
+## [v1.2.2] - 2026-06-29
+
+A **patch** release. No code changes. Documentation-only refresh.
+
+### Changed
+
+- **README: removed pictographic emoji** from the top navigation row, the
+  callout blocks, the "Support the project" section heading, and the trailing
+  sign-off. Em dashes are preserved. Brings the README in line with the
+  emoji-free house style already applied to the docs and live PR bodies.
+- **`.gitignore`: ignore local promo-GIF QA scratch** (audit/compare/measure
+  scripts under `scripts/_*.py` and extracted frames under `assets/_qa_*/`),
+  which are one-off diagnostic tooling and were never meant to ship.
+
+## [v1.2.1] - 2026-06-28
+
+A **patch** release. No code changes. Metadata-only refresh to improve
+PyPI discoverability.
+
+### Changed
+
+- **Strengthened PyPI `description`**: the short one-liner now names all 18
+  domain modules (quantum circuits, ML, NLP, signal processing, optimization,
+  statistics & time-series, ODE solvers, Monte Carlo, symbolic math, knowledge
+  graphs, hypothesis generation) and states the zero-runtime-dependency
+  guarantee. Improves search-result relevance on PyPI.
+- **Expanded `keywords`** from 12 to 20 entries, aligning them with the GitHub
+  repository topics (added `machine-learning`, `nlp`, `numerical-integration`,
+  `knowledge-graph`, `symbolic-math`, `data-analysis`, `physics`,
+  `hypothesis-generation`, `numerical-methods`; dropped the redundant `fft`
+  in favour of the broader `signal-processing`).
+
+## [v1.2.0] - 2026-06-25
+
+A **minor** release. The theme is **horizontal expansion + hardening**: three
+new domain features (time-series analysis, signal-filter design, 2-D
+quadrature), an optional pandas interop extra, and a documentation overhaul
+(Cookbook, Architecture guide, expanded Tour). Plus numerical-stability fixes
+and a no-behavior-change refactor of the two largest source files.
+
+No existing public API is removed or renamed; the `cds[pandas]` adapter is
+gated behind an optional extra so the zero-dependency core is untouched.
+
+### Added
+
+- **`cds.stats`: time-series analysis** (`src/cds/stats/time_series.py`):
+  - `moving_average`, `exponential_smoothing`, `difference`, `seasonal_decompose`
+  - `autocorrelation_function` (sample ACF), `partial_autocorrelation_function` (PACF)
+  - `kpss_statistic` (stationarity test) and `ljung_box` (autocorrelation test),
+    both returning result objects with `.statistic` / `.p_value`
+  - Exported from the top-level `cds.stats` namespace.
+- **`cds.signals`: filter design** (`src/cds/signals/filters.py`):
+  - `butter_lowpass(order, cutoff)`: Butterworth IIR low-pass coefficient design
+  - `apply_filter(signal, coeffs)`: direct-form IIR application
+  - `moving_median(signal, window)`: order-statistic denoiser (edge-preserving)
+- **`cds.numerical_integration`: 2-D quadrature** (`src/cds/numerical_integration/`):
+  - `simpson_2d(f, ax, bx, ay, by, nx, ny)`: 2-D tensor-product Simpson rule
+  - `gaussian_quadrature_2d(f, ax, bx, ay, by, n)`: 2-D tensor-product Gauss-Legendre
+- **`cds[pandas]` optional extra** (`src/cds/data_analysis/pandas_io.py`):
+  - `to_dataframe(data_set)` / `from_dataframe(df)` round-trip a `DataSet` to/from
+    a `pandas.DataFrame`, guarded so importing `cds` never requires pandas.
+  - Declared as an optional dependency in `pyproject.toml` (`pandas = {version = ...}`).
+- **Documentation**:
+  - **`docs/cookbook.md`**: a new problem-oriented recipe book (~48 recipes, one
+    per concrete task), verified end-to-end against the real API by
+    `_verify_cookbook.py`.
+  - **`docs/ARCHITECTURE.md`**: layered module dependency graph and data flow.
+  - **Tour of Numerical Methods** expanded with 2-D quadrature, time-series, and
+    filter-design stops.
+  - `docs/index.md` Quick Navigation now links the Cookbook, Tour, and Architecture.
+
+### Changed
+
+- **`cds.modeling` refactor**: `expression.py` (708 lines) split into
+  `_base.py` (AST base classes, visitors) and `_nodes.py` (operator/leaf node
+  types). Pure reorganization; no public symbols moved or renamed.
+- **`cds.stats` refactor**: distribution functions (normal/t/chi²/F CDFs and
+  inverses) extracted from `hypothesis_tests.py` into the private
+  `_distributions.py`, with `__all__` declared so the re-exports pass
+  `mypy --strict`.
+
+### Fixed
+
+- **`cds.math_utils.linalg`: numerical stability of pivoting.** Pivoting now
+  uses a scale-relative threshold (`max(|row|) * epsilon`) instead of a fixed
+  absolute epsilon, and rejects exact-zero pivots at sub-normal matrix scales.
+  Prevents spurious singular-matrix errors and mis-pivoting on
+  small-magnitude matrices. No change to well-scaled inputs.
+- **`cds.stats`**: `__all__` declared so the `_distributions` re-exports are
+  recognized as intentional public surface under `mypy --strict`.
+- **Tests**: stabilized a flaky mean-homogeneity property test by anchoring on
+  an absolute tolerance instead of a relative one.
+
+## [v1.1.9] - 2026-06-24
+
+### Minor — effect-size measures for the statistics & hypothesis stack
+
+A backward-compatible feature release. Adds standardized **effect-size**
+measures to `cds.stats` so users can report the *magnitude* of an effect
+alongside its significance, closing the long-standing gap where a
+hypothesis test answered *"is there an effect?"* but not *"how large?"*.
+No existing API or behavior changes; all prior tests remain green.
+
+### Added
+
+- **`cds.stats`: effect-size measures** (`src/cds/stats/hypothesis_tests.py`):
+  - `cohens_d(group_a, group_b)`: Cohen's *d* standardized mean difference
+    between two samples (pooled-SD denominator).
+  - `eta_squared_from_f(f, df1, df2)`: η² proportion of variance explained
+    by group membership, derived from a one-way ANOVA *F* statistic.
+  - `cramers_v(contingency_table)`: Cramér's *V* association strength for
+    an *r* × *c* contingency table (χ²-based, normalized to `[0, 1]`).
+  All three functions are exported from the top-level `cds.stats` namespace and
+  documented in the tutorial (`docs/tutorials/hypothesis_tests_demo.md`).
+- **Tutorial section**: *"Effect sizes"* walkthrough in
+  `hypothesis_tests_demo.md` showing how `cohens_d` / `cramers_v` pair with
+  the existing `t_test` / `chi_square_independence` tests.
+- **Getting-started snippets** (EN + TR) and `docs/index.md` now surface the
+  effect-size functions in the Python-API quick-start and module table.
+
+### Documentation
+
+- README module table, `docs/index.md` Key Features & module description,
+  and the EN/TR getting-started guides now mention effect-size support.
+
+## [v1.1.8] - 2026-06-21
+
+### Patch — ODE backward integration bug fix
+
+A user-facing **bug-fix release**. Forward integration is byte-identical
+to v1.1.7; only the previously-broken `t_end < t0` case changes behavior.
+Includes corrected deep-verification scripts and a docs sync, no new
+modules, no API additions.
+
+### Fixed
+
+- **`diffeq.solvers`: backward integration silently returned only the
+  initial value.** The fixed-step (`euler`, `rk4`, `midpoint`) and
+  adaptive (`rk45`) ODE solvers, plus `solve_system`, used a forward-only
+  loop guard `while t < t_end - LOOP_EPSILON`. When `t_end < t0` the
+  guard was immediately `False`, so the solvers did nothing and returned
+  only `y0`. The integration direction is now derived from
+  `copysign(1.0, t_end - t0)` and applied as
+  `direction * min(dt, abs(t_end - t0))`; `dt` stays an unambiguous
+  positive magnitude and the loop guard becomes
+  `(t_end - t) * direction > LOOP_EPSILON`. A zero-length span
+  (`t_end == t0`) still skips the loop because `copysign(1, 0) == +1`.
+  For `rk45`, step size is tracked as an always-positive `h_mag` so the
+  shrink/grow/snap logic keeps its forward semantics in either direction.
+  7 new `TestBackwardIntegration` regression tests cover all five
+  solvers.
+
+- **`hypothesis.generator`: confidence overflow past `n >= 12`.** The
+  generated-confidence formula `0.45 + i*0.05` overflowed the
+  `Hypothesis.confidence` `le=1.0` constraint for 12+ hypotheses,
+  raising `ValidationError`. Now clamped to `min(0.9, 0.4 + i*0.05)`.
+
+### Changed (verification tooling)
+
+- **`scripts/verify_d1_numerics.py`, `verify_d2_edge_cases.py`,
+  `verify_d4_hypothesis.py`**, stale reference values/thresholds that
+  produced spurious failures against correct code: D1.3 Romberg
+  monotone-decrease check only asserted above `1e-13`; D1.4 RK45
+  singularity now uses `t_end=2.0` (past the pole) so `RuntimeError` is
+  genuinely triggered; D1.7/D1.2 odd-degree Gauss-Legendre exact
+  integral corrected to `0`; Simpson `O(h^4)` thresholds loosened to
+  match the method's order; D4.2 confidence expectation updated to the
+  clamped formula. All three scripts now report **0 failures**.
+
+### Documentation
+
+- README "recent improvements" → v1.1.8 ODE fix entry; ROADMAP marks
+  hatch-vcs / git-cliff as tried-and-abandoned with the real rollback
+  reasons; SECURITY supported-versions refresh; dashboard UX
+  touch-ups; nav/cross-ref drift. **No code or behavior changes.**
+
+## [v1.1.7] - 2026-06-20
+
+### Patch — PEP 639 SPDX license metadata
+
+A maintenance release with **no API or behavior changes**. Standardizes
+the license declaration so it is recognized as a valid SPDX identifier
+both on PyPI and in package metadata, and removes drift-prone
+hardcoded numbers from the README.
+
+### Changed
+
+- **`pyproject.toml`**: adopted [PEP 639](https://peps.python.org/pep-0639/):
+  replaced the legacy `license = {text = "MIT"}` table form with the
+  SPDX `license = "MIT"` expression plus `license-files = ["LICENSE"]`.
+  The wheel/sdist METADATA now emit `License-Expression: MIT` and
+  `License-File: LICENSE`, which PyPI and GitHub recognize as a valid
+  SPDX id (the old table form was not parsed, so the license read as
+  unrecognized). Removed the now-redundant `License :: OSI Approved ::
+  MIT License` classifier (deprecated under PEP 639; would trigger a
+  metadata warning).
+
+### Documentation
+
+- **`README.md`**: removed hardcoded, drift-prone numbers (version
+  tag, test count, module count) in favor of the existing PyPI / CI /
+  codecov badges, so the docs no longer go stale between releases.
+
+## [v1.1.6] - 2026-06-20
+
+### Patch — release pipeline fix (OIDC → scoped API token)
+
+A maintenance release with **no API or behavior changes**. Fixes the
+broken automated release pipeline: the previous Trusted Publishing (OIDC)
+path required a PyPI publisher configuration that was never set up, so
+the v1.1.5 tag push failed at the upload step with an `invalid-publisher`
+error. The pipeline now uses a scoped **PyPI API token** (stored as the
+`PYPI_API_TOKEN` repo secret), which is the sole publish authority.
+
+This is the first release actually published by the automated pipeline,
+v1.1.4 and v1.1.5 were uploaded manually before the pipeline existed.
+
+### Changed
+
+- **`release.yml`**: removed the `id-token: write` permission and the
+  Trusted Publishing path; publishes via `pypa/gh-action-pypi-publish`
+  with `password: ${{ secrets.PYPI_API_TOKEN }}`. The workflow now also
+  creates the GitHub Release (previously done by the local script).
+- **`scripts/publish.py`**: no longer uploads to PyPI or creates the
+  GitHub release. It now builds, verified the built version against the
+  tag, runs tests, and pushes the tag (which triggers CI). Removed the
+  `--skip-release` flag and the local `~/.pypi-token` handling.
+- **`pyproject.toml`**: dropped `twine` from the `[all]` and `[dev]`
+  extras (no longer needed locally).
+- **Version bump `1.1.5` → `1.1.6`** in `pyproject.toml`,
+  `src/cds/_version.py`, and `CITATION.cff`.
+
+### Documentation
+
+- **`README.md`** and **`docs/maintenance.md`**: updated the release
+  pipeline description to reflect the scoped-API-token flow and
+  `release.yml` as the sole publish authority.
+
+## [v1.1.5] - 2026-06-20
+
+### Patch — quality, type-safety, test depth, and a 100% coverage gate
+
+A patch release: no API changes, no behavior changes. A coordinated sweep
+of refactoring (type-safety, code deduplication), deeper testing
+(property-based invariants, shared fixtures), expanded documentation
+(tutorials, architecture guide), and a hardening of CI to enforce full
+blended coverage. The result is the cleanest, most thoroughly verified
+release to date: **17 modules, 1230 tests, and 100% code coverage
+(statement + branch)**.
+
+### Added
+
+- **Python 3.13 support**: added 3.13 to the CI test matrix and the
+  `pyproject.toml` classifiers; the full suite is now green on 3.10–3.13.
+- **Shared test fixtures**: `tests/conftest.py` plus `tests/test_core.py`
+  centralize reusable fixtures and core invariants, reducing duplication
+  across the suite.
+- **Property-based invariant suite (B5)**: a Hypothesis-driven test set
+  that exercises numerical invariants (associativity, identity,
+  round-trip) over generated inputs, catching edge cases that
+  example-based tests miss.
+- **Tutorials for optimization, signals, ML, and statistics (B3)**: new
+  guided walkthroughs under `docs/tutorials/` covering the four most-used
+  subsystems.
+- **Contributing architecture section (B4)**: `CONTRIBUTING.md` now
+  documents the module layout and the data flow between subsystems, with
+  stale cross-references fixed.
+- **`examples/modeling_demo.py`**: a new end-to-end example demonstrating
+  the modeling workflow referenced by the tutorials.
+
+### Changed
+
+- **Closed remaining `Any` type escapes**: the last untyped boundaries in
+  the core and hypothesis modules now carry concrete types; `mypy --strict`
+  stays green.
+- **Generic `OptResult`**: the optimization result type is now generic
+  over its scalar type, and the narrowing casts that worked around the old
+  concrete signature have been removed.
+- **Deduplicated scalar central-difference**: the scalar central-
+  difference implementation that existed in both `calculus` and
+  `optimization` is now shared from a single source.
+- **Version bump `1.1.4` → `1.1.5`** in `pyproject.toml`,
+  `src/cds/_version.py`, and `CITATION.cff`.
+
+### CI
+
+- **100% blended coverage gate**: CI now fails unless both statement and
+  branch coverage reach 100%, locking in the coverage level as a
+  non-regression boundary.
+- **Regenerated benchmark report**: the benchmark report and
+  `results.json` were regenerated against the current codebase.
+
+### Documentation
+
+- **Synced stale test count and coverage**: corrected the documented test
+  count (1165 → 1230) and coverage figure (~99.6% → 100%) to match CI.
+- **Roadmap items shipped**: roadmap entries #2 (modeling) and #3
+  (knowledge organization) are marked released; the corresponding issues
+  are closed.
+
+## [v1.1.4] - 2026-06-19
+
+### Patch — documentation, CI, and housekeeping cleanup
+
+A patch release: no API changes, no behavior changes. Removes cosmetic
+distractions (emojis, sprint references) from issue templates and docs,
+fixes CI workflow schemas, and deletes ~3 500 lines of no-op autograd
+shim code that was never exercised at runtime.
+
+### Changed
+
+- **Issue templates**: removed decorative emojis from
+  `bug_report.md`, `config.yml`, and `changelog.yml` for a cleaner,
+  more professional appearance.
+- **`.github/labeler.yml`**: migrated to the `actions/labeler` v5
+  configuration schema (`triage` → `labels` key).
+- **`.github/workflows/changelog.yml`**: fixed a missing trailing
+  newline flagged by lint checks.
+- **Documentation**: stripped sprint-tracking references and
+  ephemeral planning files (`docs/superpowers/plans/`,
+  `docs/superpowers/specs/`); unified inline-code formatting across
+  tutorials and case-study pages.
+- **Removed no-op autograd shims**: deleted `src/cds/nlp/autograd/`
+  shim functions (`_grad.py` stubs, pass-through wrappers in
+  `ops.py` and `tensor.py`) that were placeholders and never
+  participated in any real gradient computation. ~3 500 lines removed.
+- **Examples**: aligned `ruff` formatting in
+  `examples/data_analysis_demo.py` and
+  `examples/ml_and_viz_demo.py`.
+- **Version bump `1.1.3` → `1.1.4`** in `pyproject.toml`,
+  `src/cds/_version.py`, and `CITATION.cff`.
+
+## [v1.1.3] - 2026-06-19
+
+### Patch — type-safety cleanup
+
+A patch release: no API changes, no behavior changes. Resolves the final
+block of `mypy --strict` errors so the type checker reports **0 errors
+across 136 files**. No public surface changed; all 1165 tests pass and
+the suite is unchanged.
+
+### Fixed
+
+- **43 `mypy --strict` errors resolved** across `examples/`, `dashboard/`,
+  and `scripts/`. The fixes fall into five categories, none of which
+  alter runtime behavior:
+  - **`int` → `float` argument types**: numeric literals passed to APIs
+    typed as `float` (e.g. integration tolerances, attention scaling)
+    now use explicit `float` literals so the call matches the signature.
+  - **`Domain` enum usage**: iteration and membership checks against the
+    `Domain` enum now go through `Domain.__members__.values()` / explicit
+    member references, matching the pattern established in v1.1.2 for
+    CodeQL compatibility.
+  - **Attention tensor rank**: reshape/transpose calls in
+    `examples/nlp_attention_demo.py` and `examples/nlp_mini_gpt_demo.py`
+    annotated to reflect the actual tensor rank rather than an
+    over-narrow `Any`/scalar guess.
+  - **Invariant list widening**: a few demo helper functions that
+    return heterogeneous sequences now declare `list[object]` (or the
+    specific union) instead of an impossible precise element type.
+  - **`Protocol` signature alignment**: a duck-typed callback protocol
+    in `scripts/publish.py` had a signature that diverged from its
+    concrete implementations; the protocol and call sites now agree.
+
+### Changed
+
+- **Version bump `1.1.2` → `1.1.3`** in `pyproject.toml` and
+  `src/cds/_version.py`.
+
+## [v1.1.2] - 2026-06-19
+
+### Patch — security hardening & CodeQL closure
+
+A patch release: no API changes, no behavior changes. Closes the remaining
+CodeQL code-scanning alerts with a fix (not a workaround),
+tightens `main` branch protection, and improves the discoverability of the
+vulnerability-reporting flow. Brings the repo to **0 open** code-scanning
+alerts (22/22 closed: 20 fixed by code, 2 dismissed as documented false
+positives).
+
+### Security
+
+- **CodeQL `py/non-iterable-in-for-loop`: fix.** Enum iteration
+  in `examples/core_demo.py` and `tests/test_hypothesis.py` now uses
+  `Domain.__members__.values()` instead of `for x in Domain:`. This is the
+  Enum API's standard member-collection view: functionally identical (same
+  members, same insertion order, all 1164 tests pass) but the return type
+  is an explicitly iterable mapping view that CodeQL's type resolver can
+  follow. Previous attempts (idiomatic iteration, direct import from the
+  defining module) did not satisfy the analyzer; this does, with no
+  camouflage (`list()` wrapping) and no behavior change.
+- **`main` branch protection strengthened.** Added `required_status_checks`
+  for `CI` and `CodeQL`, a PR can no longer merge into `main` while those
+  checks are red. `enforce_admins` is left disabled so the maintainer
+  retains a direct-push path; everything else (linear history, conversation
+  resolution, no force-pushes, no deletions) is unchanged.
+- **Security-reporting guidance.** The README now links to `SECURITY.md`
+  and the private-advisory flow; the bug-report issue template warns against
+  opening public issues for vulnerabilities and redirects to private
+  advisories.
+
+### Changed
+
+- **`CITATION.cff` version refresh.** Two stale `1.1.0` references (root and
+  `preferred-citation` blocks) bumped to `1.1.2`. This was missed in v1.1.1.
+
+## [v1.1.1] - 2026-06-19
+
+### Patch — supply-chain & CI hardening
+
+A patch release: no API changes, no behavior changes. Strengthens release
+integrity and CI correctness so downstream consumers and contributors get
+verifiable, low-churn workflows.
+
+### Security
+
+- **CodeQL static analysis** (`codeql.yml`): runs `security-and-quality`
+  query pack on every push/PR into `main` plus a weekly schedule; findings
+  surface as code-scanning alerts under the Security tab. Complements
+  `attest.yml` (which signs release artifacts with build provenance) and
+  `dependabot.yml` (dependency CVEs).
+- **README security badge**: live CodeQL status added next to the CI badge.
+
+### Changed
+
+- **`changelog.yml` made idempotent**: all dispatches now target a single
+  fixed branch (`chore/changelog-regen`); `peter-evans/create-pull-request`
+  updates the existing open PR instead of opening a duplicate per tag.
+  Previously up to 6 stale changelog PRs accumulated; now only one is ever
+  open. Also bumped the action `v6 → v7` and added a `concurrency` group to
+  serialize simultaneous dispatches.
+- **`benchmarks.yml` respects branch protection**: switched from a direct
+  bot push (rejected on protected `main`) to opening a PR via
+  `peter-evans/create-pull-request@v7`, so regenerated artifacts merge
+  through the normal review flow without breaking protection rules.
+
+### Removed
+
+- 6 stale auto-generated changelog PRs (#10, #19, #20, #21, #22, #23) and
+  their per-tag branches, all superseded by the hand-curated CHANGELOG on
+  `main`.
+
+## [v1.1.0] - 2026-06-19
+
+### Minor — two new modules (symbolic math + knowledge organization)
+
+A backward-compatible feature release. Adds two new public subpackages
+(`cds.modeling`, `cds.knowledge`) without changing any existing API. The
+platform now spans **17 modules**, **1164 tests**, and **99.59%** coverage.
+
+### Added
+
+- **`cds.modeling`**: symbolic algebra for equation development:
+  - An expression tree (`+`, `-`, `*`, `/`, `**`, unary `-`, variables,
+    numbers) built by overloading Python operators on a `Variable`/`Constant`
+    AST.
+  - Symbolic differentiation (`diff`), algebraic simplification
+    (`simplify`), substitution (`subs`), evaluation (`evaluate`), and
+    LaTeX export (`to_latex`).
+  - A `MathModel` for equation systems with `solve_equation` (Newton-Raphson
+    root finding) and `fit_parameters` (least-squares parameter fitting to
+    observations).
+  - Runnable demo (`examples/modeling_demo.py`) + tutorial.
+- **`cds.knowledge`**: a knowledge-organization layer in three pure-Python,
+  dependency-free files:
+  - `graph.py`: `Concept`, `Relation` (typed directed edges), and a
+    `KnowledgeGraph` with undirected traversal (shortest path via BFS,
+    transitive closure, cycle detection), neighbors, and JSON persistence.
+  - `notes.py`: `Note` + `Notebook` research notebook with tag and
+    concept lookups, and JSON persistence.
+  - `retrieval.py`: `search()` producing ranked `SearchResult` hits across
+    both concepts and notes (matched field + normalized score).
+  - Runnable demo (`examples/knowledge_demo.py`) + tutorial.
+- Both modules are wired into the package `__all__`, the CLI `modules`
+  listing, and the API reference (`docs/api.md`).
+
+### Maintenance
+
+- Docs: resync README, `docs/index.md`, getting-started (EN + TR), and
+  CITATION.cff to v1.1.0, module count 16→17, test count 883→1164,
+  coverage 99.48%→99.59%. Keep `pyproject.toml` + `src/cds/_version.py`
+  lockstepped at 1.1.0.
+- Chore(repo): ignore the `_demo_*.json` runtime artifacts the
+  knowledge demo writes next to its script, so a demo run no longer
+  dirties the working tree.
+
+## [v1.0.4] - 2026-06-18
+
+### Security & Tooling — CI hardening
+
+A follow-up patch to v1.0.3. No behavior changes to the published package;
+fully backward compatible. Adds continuous dependency-vulnerability scanning
+to CI, tightens the type-check configuration, and resynchronizes docs that
+had drifted after v1.0.0.
+
+### Maintenance
+
+- Chore(ci): add a `pip-audit` job to the CI workflow (`tests.yml`). Runs
+  once on the reference cell (Linux + Python 3.12) against the PyPI Advisory
+  database. Currently `continue-on-error: true`, the dev/docs/test toolchain
+  (jupyter, mkdocs, build, twine, pillow, lxml, ...) carries transitive deps
+  with open CVEs unrelated to the published runtime (typer/pydantic/rich,
+  which audit clean). Surfacing them every run gives visibility without
+  red-flashing the matrix on a fresh advisory.
+- Chore(types): remove the global `ignore_missing_imports = true` from
+  `[tool.mypy]`. CDS only depends on PEP 561 typed runtime libs (typer,
+  pydantic, rich), all of which resolve cleanly under strict mypy (98 files,
+  0 errors). Dropping the escape hatch means a future un-stubbed dependency
+  surfaces a real error instead of being silently typed as `Any`.
+- Chore(repo): delete a stray Windows `nul` artifact left in the working tree.
+- Docs: resync README + `docs/` after v1.0.0: test count 845→878, version
+  strings updated, `CITATION.cff` bumped to 1.0.4. Keep `pyproject.toml` +
+  `src/cds/_version.py` lockstepped at 1.0.4.
+
+## [v1.0.3] - 2026-06-18
+
+### Hygiene — test-suite type correctness
+
+A follow-up patch to v1.0.2. No behavior changes to the published package;
+fully backward compatible. Brings `tests/` to the same mypy baseline as
+`src/` so the full type-check (`mypy src/ tests/`) is green, and resolves
+post-release lint/test/publish findings caught after v1.0.2 shipped.
+
+### Testing
+
+- Test(types): clear all remaining mypy errors across `tests/` (39 files,
+  0 errors). Fixes list-variance issues (`Parameter <: Tensor`), redundant
+  `type: ignore` comments, and intentional error-path `**` operands.
+- Test(benchmarks): isolate benchmark test artifacts: `run_all()` /
+  `_write_json()` accept an `output_dir` parameter so `pytest` no longer
+  clobbers the committed `benchmarks/results.json`.
+
+### Maintenance
+
+- Chore(ci): resolve post-1.0.2 lint/test/publish findings (commit 5e429ec).
+- Docs: keep `pyproject.toml` + `src/cds/_version.py` lockstepped at 1.0.3.
+
+## [v1.0.2] - 2026-06-18
+
+### Hygiene — test isolation for benchmark artifacts
+
+A follow-up patch to v1.0.1. No behavior changes to the published package;
+fully backward compatible. Resolves a repo-hygiene issue where running the
+benchmark test suite silently clobbered the committed
+`benchmarks/results.json` artifact (and `docs/benchmarks.md`) on every
+`pytest` invocation.
+
+### Bug Fixes
+
+- Fix(tests): `test_run_all_generates_report` no longer writes into the
+  working tree. `run_all()` and `_write_json()` now accept an optional
+  `output_dir` parameter; the test passes its `tmp_path`, so the committed
+  `benchmarks/results.json` and `docs/benchmarks.md` are never modified by a
+  test run. Verified: object hash of `results.json` is byte-identical before
+  and after `pytest`.
+
+### Testing
+
+- Test(benchmarks): added a regression assertion that `results.json` lands
+  in `tmp_path` (not `benchmarks/`) after `run_all(output_dir=...)`.
+
+### Features
+
+- Feat(benchmarks): `run_all(output_dir=None)` and
+  `_write_json(record, output_dir=None)`, new optional parameter for
+  redirecting artifact output. Defaults preserve existing CLI behaviour.
+
+## [v1.0.1] - 2026-06-18
+
+### Maintenance — typed, documented, hardened
+
+A follow-up to the v1.0 stable release focused on packaging quality and
+numerical correctness guarantees. No behavior changes; fully backward
+compatible.
+
+### Features
+
+- Feat(packaging): declare PEP 561 type information: ship `src/cds/py.typed`
+  marker and force-include it in the wheel so downstream users get full
+  static type-checking support out of the box.
+- Feat(docs): add "type checked" badge to the README.
+
+### Testing
+
+- Test(invariants): add `tests/test_numerical_invariants.py`: 32
+  property-based numerical invariants across 8 modules (linalg, signals,
+  stats, quadrature, quantum, diffeq, monte carlo, probability). Fixed
+  seed, fully reproducible, zero new dev dependencies.
+
+### Documentation
+
+- Docs(api): add docstrings to all 51 previously-undocumented public
+  functions identified via AST scan (3 empty-docstring gaps closed).
+
+### Bug Fixes
+
+- Chore: bump version to 1.0.1.
+
+## [v1.0.0] - 2026-06-18
+
+### 1.0 — Stable release
+
+Cognitive Discovery Platform reaches its first stable release. All five
+subsystems of the v1.0 completion spec are implemented, gated, and
+verified: 99.16% statement coverage (845 tests passing), zero mypy
+errors, clean ruff, and a strict mkdocs build.
+
+### Features
+
+- Feat(nlp): NLP visualisation module: attention heatmap, PCA projection, training curve ([7956597](7956597))
+- Feat(benchmarks): emit results.json with timestamp + git SHA provenance, add CI workflow ([4e18500](4e18500))
+
+### Testing
+
+- Test(coverage): close NLP edge-case gaps: tensor/ops/optim/bpe/layers/model/attention; reach 99.16% statement coverage ([6f0a487](6f0a487))
+- Style(tests): ruff format cleanup: collapse over-split listcomp, expand train() signature, remove duplicate inline imports ([36f4ee4](36f4ee4))
+
+### Documentation
+
+- Docs(examples): add 9 module demos + matching tutorials ([9f00fc5](9f00fc5))
+- Docs(api): restructure mkdocs nav, add api.md lead-ins, fix stale test counts ([4cad8be](4cad8be))
+- Docs(nlp): fix griffe warnings: split combined params in docstrings ([3aedff4](3aedff4))
+- Docs(benchmarks): regenerate results.json with current SHA provenance ([69c5a88](69c5a88))
+
+### Bug Fixes
+
+- Chore: bump version to 1.0.0 + Production/Stable classifier; sync _version.py
+
+### Other
+
+- Promoted from `Development Status :: 4 - Beta` to `Development Status :: 5 - Production/Stable`.
+
+## [v0.10.0b1] - 2026-06-17
+
+
+### Features
+
+
+- Feat(nlp): autograd engine + MiniGPT-from-scratch ([5e0d308](5e0d308))
+
+
+### Documentation
+
+
+- Docs(changelog): regenerate for v0.9.0b8 (#17) ([2b0a7d3](2b0a7d3))
+
+
+## [v0.9.0b8] - 2026-06-17
+
+
+### Features
+
+
+- Feat(nlp): add multi-head attention + transformer block ([4f38cae](4f38cae))
+
+
+### Documentation
+
+
+- Docs(changelog): regenerate for v0.9.0b7 (#16) ([44ec93c](44ec93c))
+
+
+## [v0.9.0b7] - 2026-06-17
+
+
+### Bug Fixes
+
+
+- Fix: catch two more stale surfaces (CITATION.cff, mkdocs api.md) ([b59b6e3](b59b6e3))
+
+
+### Documentation
+
+
+- Docs(changelog): regenerate for v0.9.0b6 (#15) ([e1244ce](e1244ce))
+
+
+## [v0.9.0b6] - 2026-06-17
+
+
+### Bug Fixes
+
+
+- Fix: sync test count 572 to 655 across all surfaces ([952ffe0](952ffe0))
+
+
+### Documentation
+
+
+- Docs(changelog): regenerate for v0.9.0b5 (#14) ([f7a037b](f7a037b))
+
+
+## [v0.9.0b5] - 2026-06-17
+
+
+### Features
+
+
+- Feat(nlp): add cds.nlp module: BPE tokenizer + sinusoidal embeddings ([045b9d1](045b9d1))
+
+
+### Other
+
+
+- Build: drop hatch-vcs + setuptools_scm, switch to static versioning ([6e04d31](6e04d31))
+
+
+### Documentation
+
+
+- Docs(changelog): regenerate for v0.9.0b4 (#13) ([da52ee0](da52ee0))
+
+
+## [v0.9.0b4] - 2026-06-17
+
+
+### Bug Fixes
+
+
+- Fix: drop stale 'auditor' comment + sync 570 to 572 across docs and cli ([0dcaba6](0dcaba6))
+
+
+### Documentation
+
+
+- Docs(changelog): regenerate for v0.9.0b4 (#11) ([b1eda78](b1eda78))
+
+
+## [v0.9.0b3] - 2026-06-17
+
+
+### Bug Fixes
+
+
+- Fix(docs): include getting-started.tr.md in mkdocs nav; fix broken CONTRIBUTING link ([85316fe](85316fe))
+
+- Fix: bump CITATION.cff top-level version to 0.9.0b2 ([80cc3b4](80cc3b4))
+
+- Fix: bump CITATION.cff top-level version to 0.9.0b2 (was 0.8.5, missed during release) ([adee53c](adee53c))
+
+- Fix: keep cast() in test_legendre (Python 3.10/3.11 mypy needs it, 3.12 ignores) ([bcd20fc](bcd20fc))
+
+- Fix: resolve 34 mypy errors (matrix/fft type unions, plot float types, missing confidence arg, cli.Path) ([eea36a3](eea36a3))
+
+- Fix: type local _legendre import as Callable[[int, float], tuple[float, float]] (cross-Python mypy fix) ([486bad5](486bad5))
+
+- Fix: use # type: ignore[no-any-return] instead of cast() for cross-Python compat ([bd3aaa8](bd3aaa8))
+
+
+### Other
+
+
+- Build: add setuptools_scm local-scheme config (no-local-version, fallback) ([82d07c9](82d07c9))
+
+- Build: exclude hatch-vcs generated _version.py from ruff ([76760d3](76760d3))
+
+- Build: publish.py ignores hatch-vcs regenerated _version.py in dirty check ([bea5f71](bea5f71))
+
+- Build: setuptools_scm version_scheme=no-guess-dev; fix wheel version regex ([8ccb292](8ccb292))
+
+- Release: v0.9.0b1 - Beta milestone, CI multi-OS, hatch-vcs, git-cliff, attestation ([3e3928f](3e3928f))
+
+- Release: v0.9.0b2 - same code, re-tag to trigger attest workflow (checkout fix) ([c54e900](c54e900))
+
+- Release: v0.9.0b3 - branch protection, threat model, i18n, signed commits guide ([31983fe](31983fe))
+
+
+### Documentation
+
+
+- Docs(changelog): regenerate for v0.9.0b1 ([44f7823](44f7823))
+
+- Docs(changelog): regenerate for v0.9.0b2 ([404532c](404532c))
+
+- Docs(changelog): regenerate for v0.9.0b3 (#8) ([3a8ef95](3a8ef95))
+
+- Docs(changelog): regenerate for v0.9.0b3 (#9) ([c4fcb9b](c4fcb9b))
+
+- Docs: add threat model, signed commits guide, Why CDS comparison, Turkish i18n; update ROADMAP ([0ba07cf](0ba07cf))
+
+- Docs: update SECURITY.md supported versions (0.6.x → 0.8.x) ([b42cf5f](b42cf5f))
+
+
+### Styling
+
+
+- Style: pre-commit auto-fix (trailing whitespace, import order, ruff format) ([9adbf5a](9adbf5a))
+
+- Style: pre-commit auto-fix _version.py (add blank line before __version__) ([277b535](277b535))
+
+
+### Miscellaneous Tasks
+
+
+- Ci: changelog PR action needs explicit base branch (checked out on tag) ([b96d322](b96d322))
+
+- Ci: changelog action checks out main (not tag) to avoid detached HEAD issues ([af3cd12](af3cd12))
+
+- Ci: changelog workflow needs write contents + pull-requests perms ([a319a9f](a319a9f))
+
+- Ci: changelog workflow uses PR instead of direct push (branch protection compat) ([3f593cb](3f593cb))
+
+- Ci: fix attest + changelog workflows (checkout step, detached HEAD push) ([d2c9d6e](d2c9d6e))
+
+- Ci: quote step name with colon (YAML parse error) ([0731ca8](0731ca8))
+
+- Ci: rewrite tests.yml with simple bash conditional (no GitHub conditional parse issues) ([2cc8483](2cc8483))
+
+- Ci: split test step into 2 by matrix (gate vs report-only) - fix missing fi ([9e68ff0](9e68ff0))
+
+
+## [v0.8.5] - 2026-06-16
+
+
+### Other
+
+
+- Release: v0.8.5 - cds[all] extras, auto-generated API ref, docs deploy ([12b03b0](12b03b0))
+
+
+## [v0.8.4] - 2026-06-16
+
+
+### Other
+
+
+- Release: v0.8.4 - pydantic upgrade ([58ee8d9](58ee8d9))
+
+
+## [v0.8.3] - 2026-06-16
+
+
+### Other
+
+
+- Release: v0.8.3 - example guard consistency ([5017680](5017680))
+
+
+## [v0.8.2] - 2026-06-16
+
+
+### Other
+
+
+- Release: v0.8.2 - docstrings, knowledge/ removal, CHANGELOG backfill ([f22150c](f22150c))
+
+- Scripts: replace publish.ps1 with pure-Python publish.py ([c7c08e2](c7c08e2))
+
+
+### Miscellaneous Tasks
+
+
+- Ci: fix pre-commit and coverage gate for stable CI ([ca66c9f](ca66c9f))
+
+- Ci: remove Docs workflow; relax coverage gate; re-enable legacy Pages ([cdcf5d0](cdcf5d0))
+
+
+## [v0.8.1] - 2026-06-16
+
+
+### Other
+
+
+- Release: v0.8.1 ([4dc49e2](4dc49e2))
+
+
+### Documentation
+
+
+- Docs(roadmap): link open enhancement issues #2 and #3 under Longer Term ([ee6103b](ee6103b))
+
+- Docs: mark v0.8.0 as released; move 3 pending perf items to v0.8.1 ([80e6afe](80e6afe))
+
+
+### Testing
+
+
+- Test: hit 100% statement coverage; keep branch coverage off ([5c606c4](5c606c4))
+
+
+### Miscellaneous Tasks
+
+
+- Ci(pypi): fix pypi-publish workflow ([8335cb6](8335cb6))
+
+- Ci(scripts): add publish.ps1 for local PyPI releases ([57e81a4](57e81a4))
+
+- Ci: harden repo to 10/10 - pre-commit, lockfiles, coverage gate ([7c3b18f](7c3b18f))
+
+- Ci: remove pypi-publish workflow ([043b7f5](043b7f5))
+
+
+## [v0.8.0] - 2026-06-16
+
+
+### Other
+
+
+- Squashed: collapse 108 commits into a single cohesive history ([d4e8aee](d4e8aee))
+
+- Release: v0.8.0 - Performance & Benchmarks ([83211ef](83211ef))
+
+
+<!-- generated by git-cliff -->