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Changelog

All notable changes to OpenTIMS: the C++ core (opentims++), the Python package (opentimspy) and the R package (opentimsr), which share one version number. R versions carry no pre-release suffix, so 1.2.0b4 was opentimsr 1.2.0.

Each release’s section becomes the notes of its GitHub release, and src/opentimsr/NEWS.md points here, so R’s news() shows it too.

1.2.3 (2026-11-03)

Core

• The shared C++ library installs NOTICE (licences of the bundled SQLite, Zstandard and mio) next to its licence.

Python

• Package metadata gives the licence as the SPDX expression MIT (PEP 639) instead of the full licence text; LICENCE and the new NOTICE (licences of the bundled SQLite, Zstandard and mio) ship in the wheel. Building from source needs scikit-build-core 0.11 or newer.

R

• OpenTIMS() on a folder without analysis.tdf stops with “No analysis.tdf in ” before opening a database connection, instead of RSQLite’s “Could not connect to database” (which also leaked memory; CRAN’s valgrind check would report it).

1.2.2 (2026-10-25)

Core

• Extraction decodes frames in parallel, and decodes a frame requested several times only once.
• Optional lookup tables for Bruker’s m/z and 1/K0 conversion, much faster when converting many peaks; calls into Bruker’s library are serialised.
• Compressed frame headers are read without unaligned loads (undefined behaviour reported by CRAN’s sanitizer checks).
• Errors from parallel decoding keep their message when R loads both libc++ and libstdc++ (CRAN’s fedora-clang check reported “c++ exception (unknown reason)”).
• Repeated frames are extracted correctly in every column, and zstd flag overrides are honoured.
• The public header no longer includes SQLite, so consumers of the shared library need no SQLite headers.

Python

• get_separate_frames() decodes each frame once.
• query() and frame_arrays() reject fractional, negative and out-of-range frame ids instead of truncating them.
• SQLite connections are closed, framesTIC is cached per instance, and invalid input raises exceptions instead of failing asserts.
• Docstrings of the conversion and retention-time functions describe what the code does.
• Requires Python 3.9 or later; pybind11 is no longer a runtime dependency.

R

• Back on CRAN: the README installs it with install.packages("opentimsr").
• New get_separate_frames().
• Frames are decoded straight into R vectors.
• download_bruker_proprietary_code() reuses a library already downloaded (new argument overwrite) and never rewrites one in place: downloading it a second time in a session no longer crashes R (#21).
• Addressed CRAN’s review of 2026-10-06: Title and Description wording, the length(), range() and [ methods are exported, and examples that download Bruker’s library use \donttest{} and write to tempdir().

1.2.1 (2026-10-03)

Core

• Frame extraction is thread-safe; cached frames no longer alias one buffer, and failed extraction joins its workers and restores the threading state.
• Frame ids are no longer assumed to run 1..N.
• Hardened against corrupted data: decompressed sizes are checked before allocation, unexpected dataset contents raise exceptions instead of failing asserts, and slice counters cannot wrap.
• Locale-independent number parsing, without side effects on the global locale.
• Frame counts are parsed as 64-bit on Windows; dlopen’ed SQLite symbols are resolved thread-safely; an SQLite busy timeout lets concurrent readers open the same dataset.
• Corrected intensities are clamped into the uint32 range.
• Conversion failures raise exceptions with Bruker’s diagnostics.
• A C++ test suite, run in CI with sanitizers, Valgrind and fuzzing.

Python

• Frame owners are kept alive while frame references exist.
• query() with _sanitize=False fills user-provided arrays.

R

• Links the system zstd and no longer bundles zstd or SQLite; SQLite access goes through RSQLite.
• Mateusz Łącki is the maintainer.
• Frame numbers and slices are validated with clear errors; range() with by = 0 no longer loops forever.
• OpenTIMS() expands ~ and relative paths, and opens analysis.tdf read-only.
• download_bruker_proprietary_code() stops clearly on platforms without Bruker’s library.
• Released on GitHub as a source tarball and a Windows binary.

1.2.0 (2026-04-22)

• Built-in open-source m/z and 1/K0 converters, selectable per dataset, as an alternative to Bruker’s library.
• Reworked build system: static and shared C++ libraries with CMake and pkg-config files; SQLite loaded from Python’s own module or linked.
• Reworked R bindings with tests.
• Datasets whose frame ids do not start at 1 are supported.
• Asserts replaced by exceptions.

Earlier releases are described only by the git history.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.