Changes in version 0.0.0.9000                      

Development version; nothing has been released yet.

Package skeleton (task T01)

  - New package skeleton at the repository root: DESCRIPTION,
    roxygen-generated NAMESPACE, GPL (>= 3) licence, testthat 3rd
    edition, a getting-started vignette and a pkgdown configuration that
    builds into site/ with the themakR template.
  - library(qupflowR) loads no optional package and starts no Java,
    QuPath, Python or browser process. Optional packages are checked
    where they are used, with a qp_capability_error (code
    CAPABILITY_UNAVAILABLE) that names the missing packages.
  - Skip helpers for future integration tests detect QuPath, Java, the
    bridge artefact, an isolated display, a project-local browser and a
    Python profile without touching user profiles, and record
    machine-readable skip reasons. So far only their own unit tests use
    them.
  - Package foundations: classified error conditions with one error code
    registry shared with the Java bridge, a German and English message
    catalogue, protocol JSON helpers with canonical JSON, and a JSON
    Schema subset validator with the protocol schemas and their shared
    fixture corpus. JSON text with comments, with form feed or vertical
    tab between tokens, or with an unterminated string (also after a
    complete value, as in [1]") is rejected (JSON_INVALID, reason
    syntax), as in the Java bridge. The checks before parsing find
    string literals in one linear pass, so a long unterminated string of
    escaped quotation marks is rejected at once instead of taking
    minutes.
  - Measurement names may be empty strings: QuPath stores such names and
    the protocol keeps names byte-exact.
  - The schema set annotatr-control/v1 defines the capability vocabulary
    of the optional annotatR integration: the profiles I0 to I4, their
    states and reason codes. The control profiles I2 and I3 can only be
    unsupported or planned until an annotatR release publishes its
    control contract. There is no annotatR adapter in this version.
  - Quality tooling: thin GitHub Actions callers of the shared CTTIR
    workflows pinned to commit d54cd50, the shared .lintr, and
    tools/quality.R as the local equivalent: blocking lint without
    silent exclusions or # nolint markers, tests-only coverage with a
    floor of 90 % and a committed baseline that must not drop, and a
    public API inventory whose history is checked.
  - renv.lock records the development library used for this version;
    renv is not activated for the project. Two entries cannot be
    restored with renv::restore(): annotatR 0.0.1 and themakR 0.1.0 were
    installed from local sources, so the lock file has no repository or
    commit for them.

Dependency decisions

  - R (>= 4.5.0). R CMD check --as-cran passes with R 4.6.1 and with
    R 4.5.3. R patch releases add no features, so these checks cover
    the 4.5 and 4.6 series. R 4.5 is the oldrel-1 job of the shared
    CTTIR check workflow, the oldest blocking job there; an older
    minimum will be declared only after a check on that version.
  - Imports holds only packages that the package code uses today: cli,
    jsonlite, stats, tibble and utils. Unused Imports produce an R CMD
    check NOTE, so the other planned core dependencies wait in Suggests
    and move to Imports together with the code that needs them: httr2
    with the bridge client (T02); processx, callr, R6 and fs with worker
    control, connections and path handling (T03); digest and zip with
    workflow storage (T15, where SHA-256 digests are computed). digest
    is already used by the tests and the development scripts. The base
    package tools is added when code uses it.
  - annotatR is an optional partner package in Suggests. It is not on
    CRAN, so Remotes points to its GitHub repository for development
    installs; those install its current development version, not the
    local 0.0.1 recorded in renv.lock.