Conatus 0.1.2

A correction release for the findings of an external review of 0.1.1 and of a review of its
documentation. Each fix has a test against an independent reference value. Upgrading is
recommended: some results of 0.1.1 were wrong (see Correctness). Results that can differ from
0.1.1: large finite eigenvalues of dense QZ, parametric pencils with small parameter terms,
contour results with close roots, critical(over=) and the Hopf curves of continue_codim2.

Security

• Local Studio: the session cookie is cn_session_<port> with --local and __Host-cn_session
  over HTTPS, and each session is bound to the Host it was opened at. The cookie was valid when
  replayed from any port of 127.0.0.1. On plain HTTP, another service on the same host name and
  port can still read it; the Studio guide says so.
• Telemetry spools, Studio audit logs and token files are created 0600 in 0700 directories,
  whatever the umask; they took the umask's mode. Run records and outputs keep the umask's mode.
• hub serve --local --state hub_state uses the directory given; the explicit spelling of the
  default was replaced by a temporary directory.

Correctness

• Dense QZ (solve_dense, m.eigenvalues(method="dense")): with a nonsingular M every
  eigenvalue is finite and returned; L = -diag(1, 1e13), M = I lost 1e13 as infinite. The
  rank of M is measured on M as given, so a row of rounding noise where M has a zero row
  does not make M look nonsingular (its infinite eigenvalue was returned as a finite value near
  1e17). The log states the rank and names the pairs it cannot classify.
• Parametric pencils (m.parametric): a coefficient entry is discarded only at rounding level
  for that entry; a whole matrix 1e-14 times the pencil's largest entry was deleted as
  "identically zero" (eigenvalue 1e-14 r read 0 at r = 1e14). An evaluation where the discarded
  entries could matter is refused.
• continue_codim2(kind="hopf") stops at the Bogdanov–Takens point (κ = ω² = 0) and keeps only
  points whose Jacobian has the pair ±iω; it continued into real-saddle points. Tutorial 10, its
  figure and its checks are corrected.
• cn.contour.beyn: close distinct roots (0.2 and 0.2000001) are returned separately, each
  counted on its own square; they were one root "of multiplicity 2" at their mean.
  multiplicity is the number of eigenvalues in a square of half-side enclosure (new field)
  around each value.
• cn.contour.beyn(counted=...) refuses a count of another operator (it evaluates det T again
  at points the count recorded); it accepted any count of the same box.
• cn.contour.count is described as a test on samples of the boundary. For a function T(z)
  with poles, a zero and a pole on opposite sides of the boundary, closer to it than a step, are
  not seen; count_method, explain() and the new CountResult.scope and
  poles_by_construction say so. The contour results no longer use the word "certified".
• BeynResult.residual_definition states the scale of the residuals; the guide's formula for a
  function T(z) was not the one computed.
• critical(over=) computes the neutral value at over_points points of the interval (default
  9) and refines every local minimum of that scan; one bounded Brent search could return a higher
  local minimum as the critical value. The log lists the minima found, and a point where the
  pencil is refused is logged as unchecked.
• The run cache refuses a function whose code reads a value chosen at run time (getattr,
  vars, os.environ, open, np.load, ...); such a read kept the cache key, and a changed
  configuration returned the old value.

Checks that reported success without measuring it

• verify() measures the right and left residuals of the vectors the mode holds when it is
  called; it printed the residual stored by track(), so a mode whose vector had been changed
  still passed. A zero vector, or a vector of the wrong size, is not a pass. A point where the
  parametric pencil is refused is reported as a failed check instead of an exception.
• resolution_report is ok only when every variable of the plan was measured; an empty or
  partial state is reported as not measured (complete, unmeasured). An array of the wrong
  shape is refused with the expected shape instead of an IndexError.
• python -m conatus agent check checks the argument values of Simulation.run and
  IVPSolver.run at the stop (run(steps=-1) was reported ok); the new validated field says
  whether the values of the stopped call were checked.
• The acceptance scripts shipped with the package check the mathematical requirement of each
  case, and their runner counts a script that crashes or prints no result as a failure.
• uncertainty(...).explain() prints tuple resolutions such as N=[(8, 8), (12, 12), (16, 16)]
  (it raised TypeError).

Documentation and website

• The home page and the README start with one complete calculation, the critical Reynolds number
  of plane Poiseuille flow, shown with its recorded output. The site and the documentation share
  one navigation and one getting-started route.
• The code shown on the guide and tutorial pages runs when copied in order, and the outputs shown
  are what it prints; a test runs every page.
• Tutorial figures redrawn: tables where a plot carried little information, captions computed
  from the plotted data, values below the axis floor drawn as upper limits.
• Wording: claims are stated with their scope and threshold, without slogans; the time-stepper
  orders are given per scheme; the pages no longer compare Conatus with other codes.
• The Validation page lists published values and closed forms; the values are labelled as
  reported by the author, since their run records are not public.
• Pages no longer cite examples or test files that the package does not ship; the deprecation
  versions and the release status are read from the package.
• SHA256SUMS lists bare file names, so sha256sum -c SHA256SUMS works in the directory that
  holds the downloaded wheels.

Known limitations

• Unchanged from 0.1.1 (see below).
• A contour count for a user function T(z) with poles is a test on samples, not a proof.
• Local Studio over plain HTTP: another service on the same host name and port can replay the
  session cookie.
• Dense QZ: a pencil whose M is singular and which also has finite eigenvalues larger than
  about 1e12 times the scale of the pencil can have pairs that cannot be classified; they are
  kept as finite and named in the log.