NEWS

qupflowR 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.