Added scales to the dependency bootstrap inventory so clean development containers and dependency audits match the package DESCRIPTION metadata, repaired Grammateus report-contract expectations for the current testthat release, and added package URL metadata for clean pkgdown builds.
floundeR 0.21.18
Started the release-preparation checkpoint after completing the reboot documentation refresh, with version and NEWS metadata aligned before the remaining test, check, and documentation-build tasks.
floundeR 0.21.17
Added report-card plot examples to the Grammateus technical-report vignette, including governed status-count and per-check status figures for report contracts.
floundeR 0.21.16
Added source pkgdown navigation for the rebooted documentation set, grouping contemporary POD5, BAM, Synoptikon, Grammateus, Rust, and library-preparation reference surfaces ahead of retained legacy helpers.
floundeR 0.21.15
Added a two-direction Grammateus plot vignette showing analyst-owned R ggplot2 figures being wrapped into report contracts and Grammateus semantic plot specs being rendered by the controlled R backend.
floundeR 0.21.14
Added a Grammateus technical-report vignette that builds a runtime-free semantic QC report contract, governed figure wrapper, Mnemosyne theme descriptor, manifest, and runtime-gated HTML/PDF rendering path.
floundeR 0.21.13
Added a focused derived-POD5 demonstration artifact guide covering the maintained opt-in workflow, produced provenance metadata, repository policy, and Synoptikon/reporting use of pod5-tools-derived subset or split artifacts.
floundeR 0.21.12
Promoted the ONT Zymo fecal POD5 source and selected pass/fail objects as the canonical opt-in real-data examples across README, dataset policy, and POD5 vignette guidance.
floundeR 0.21.11
Added contemporary package vignettes for POD5 QC and BAM QC, and refreshed the Synoptikon handoff vignette so the active tutorial set covers POD5 provenance, curated Bamana-backed BAM evidence, and sectioned QC JSON handoff without restoring retired FAST5 workflows.
floundeR 0.21.10
Added an offline “run health in one minute” README example that produces a run summary, report-card counts, and Synoptikon payload schema check from a sequencing-summary input.
floundeR 0.21.9
Rewrote the README around the contemporary nanopore QC workflow, covering sequencing-summary contracts, POD5 evidence, BAM QC, library-preparation evidence, Synoptikon handoff, and optional Grammateus reporting boundaries.
floundeR 0.21.8
Verified and recorded the current Bioconductor policy posture for optional Grammateus runtime assets, external system requirements, downloads, data, tests, and future submission blockers.
floundeR 0.21.7
Documented the GitHub installation paths for public open-source floundeR users and authorized users configuring optional prebuilt Grammateus runtime assets.
floundeR 0.21.6
Added disabled GitHub Actions templates that separate public floundeR checks without Grammateus from manual credentialed Grammateus runtime/report-rendering checks, preserving the temporary Actions-disabled posture during code churn.
floundeR 0.21.5
Added release-level Grammateus runtime compatibility manifest checks so runtime validation fails when the compatibility asset is missing, unsigned, version-mismatched, or declares a floundeR compatibility window that disagrees with manifest.json.
floundeR 0.21.4
Tightened Grammateus runtime validation so declared private runtime signature files are path-safe, present, non-empty, and checksum-verified when manifests provide signature SHA-256 values.
floundeR 0.21.3
Defined the GitHub/private release asset names, platform identifiers, runtime index, compatibility manifest, and publication rules for prebuilt Grammateus runtime bundles.
floundeR 0.21.2
Documented the legacy RMarkdown boundary: RMarkdown is retained for package vignettes and transitional documentation only, while production QC reports must use Grammateus semantic report contracts and runtime rendering.
floundeR 0.21.1
Added report-contract regression coverage for Grammateus element schemas, required captions and alt text, provenance hashes, stable identifiers, and serialized qc_report() contract/manifest handoff fields.
floundeR 0.21.0
Added the first Grammateus QC plot helper set for yield over time, read quality, read length, flowcell density, barcode balance, POD5 integrity, BAM mapping, BAM MAPQ, and BAM flag summaries.
floundeR 0.20.0
Added qc_report() to assemble Grammateus-backed nanopore QC report contracts, manifests, Mnemosyne theme metadata, governed figures, requested HTML/PDF output status, and provenance while keeping private Grammateus runtime rendering optional.
floundeR 0.19.0
Added grammateus_mnemosyne_theme() and grammateus_apply_theme() to encode Mnemosyne Biosciences Grammateus template/theme metadata, style policy, and themed report assembly without bundling private Grammateus runtime assets.
Added regression coverage confirming core QC APIs, Synoptikon export, and package checks remain usable without private Grammateus runtime assets.
floundeR 0.17.0
Added Grammateus runtime discovery, manifest parsing, validation, version, availability, and cache-install helpers for optional private prebuilt runtime bundles. Core floundeR remains installable without Grammateus assets.
floundeR 0.16.1
Defined the prebuilt Grammateus runtime interface for public floundeR builds, including the runtime bundle layout, manifest schema, discovery order, validation categories, security checks, and Rust response envelope expected when private Grammateus source is unavailable.
Made Rust capability parsing feature-set based so optional engines such as Porkchop and Grammateus can be reported independently of their order in the native capability payload.
floundeR 0.15.0
Added grammateus_plot_spec() and grammateus_render_plot() to support Grammateus-to-R controlled plot generation from semantic ReportPlot-shaped specs, including deterministic run directories, generated R scripts, plot/data/script hashes, backend session capture, and PNG/SVG artifact metadata.
floundeR 0.14.0
Added grammateus_figure_from_ggplot() and grammateus_figure_from_file() so existing ggplot2 plots and PNG/SVG artifacts can be handed to the Grammateus reporting path as governed figure objects with deterministic artifact paths, SHA-256 checksums, captions, alt text, methods notes, dimensions, and provenance.
floundeR 0.13.4
Identified the Grammateus public Rust APIs floundeR should use for semantic tables, figures, controlled R plots, HTML/PDF rendering, trusted-report manifests, provenance tables, lifecycle metadata, governance envelopes, branding hooks, and optional runtime integration.
Recorded the Grammateus APIs that should remain out of normal floundeR bindings so the reporting surface stays focused on nanopore QC and Synoptikon handoff rather than becoming a general Grammateus frontend.
floundeR 0.13.3
Recorded Grammateus canonical charter, SRS, ARD, rendering-elements, and trusted-report contract verification before report-binding work, including the constraints floundeR must preserve for internal-only branding, deterministic semantic elements, provenance, Synoptikon/Mneion trust reuse, and optional private runtime distribution.
floundeR 0.13.2
Recorded the Grammateus checkout preflight for Slice 13: the private local ../grammateus source checkout was clean, current with origin/main, and not added as a public floundeR build dependency.
floundeR 0.13.1
Documented the Porkchop capabilities that remain out of scope for normal floundeR APIs, including read trimming, transformed FASTQ output, barcode demultiplexing, cDNA rescue, benchmarking, terminal dashboards, standalone HTML reports, custom ungoverned motif registries, and raw CLI passthrough.
Added in-process Porkchop-backed R wrappers for library kit candidates, adapter/primer evidence, barcode/flank evidence, and cDNA primer-pair evidence. Until Porkchop is public, default source builds keep that engine unlinked and the wrappers fail with typed R conditions; local sibling-checkout builds can enable the porkchop-integration feature.
Porkchop evidence preserves heuristic score terminology, kit provenance, lifecycle/support status, and validation limitations while keeping trimming and preprocessing out of the normal floundeR API.
floundeR 0.11.4
Added the Porkchop integration audit for curated library-preparation QC surfaces, preserving heuristic score terminology and excluding trimming-first APIs from the normal floundeR surface.
floundeR 0.11.3
Added an executable Synoptikon QC handoff vignette covering run QC evidence, ONT POD5 provenance, reserved BAM/library-preparation sections, and JSON payload writing.
Updated the release-tarball check to build and check package vignettes.
floundeR 0.11.2
Added offline Synoptikon QC payload JSON-schema validation tests and fixed nested provenance metadata plus report-card check schema compatibility.
floundeR 0.11.1
Strengthened Synoptikon QC payload section handling so supplied flowcell, barcode, POD5, BAM, and library-preparation evidence contributes section status and is covered by offline tests.
floundeR 0.11.0
Added as_synoptikon_qc() and write_synoptikon_qc() to assemble existing floundeR QC evidence into the v1 Synoptikon payload contract and write it as JSON for downstream ingestion.
floundeR 0.10.0
Defined the first versioned Synoptikon QC payload contract and installed the v1 JSON schema for downstream ingestion, review, reporting, and audit handoff work.
floundeR 0.9.2
Documented Bamana capabilities that remain out of scope for floundeR so the BAM surface stays curated around nanopore QC, review, provenance, reporting, and synoptikon handoff rather than becoming a wholesale Bamana mirror.
floundeR 0.9.1
Documented the Bamana read-only versus transformation boundary, including which operations may feed QC evidence directly and which write-capable operations require explicit output paths and provenance manifests.
floundeR 0.9.0
Added bam_qc_report_card() and bam_qc_report_card_thresholds() to convert Bamana-derived summary, index, sort, tag, EOF, validation, and provenance evidence into the standard floundeR pass/warn/fail report-card schema.
floundeR 0.8.1
Documented and tested Bamana response-envelope semantics: payload-bearing QC failures remain structured evidence, while no-payload failures become typed R conditions carrying Bamana code, detail, and hint metadata.
Added Rust-backed bam_verify(), bam_validate(), and bam_check_eof() wrappers over Bamana’s read-only verification, validation, and BGZF EOF evidence surfaces, with stable R-native return shapes and offline BAM fixture coverage.
floundeR 0.6.0
Added Rust-backed bam_summary() as the first curated Bamana integration, returning stable R-native QC tables for command status, evidence scope, header metadata, counts, fractions, MAPQ, mapping state, flags, references, index-derived evidence, and optional MAPQ histograms.
floundeR 0.5.2
Audited Bamana’s public Rust command modules, JSON contracts, and governing docs, and recorded the curated read-only BAM QC/review surface that should be promoted into floundeR through in-process Rust bindings.
floundeR 0.5.1
Added an opt-in derived-POD5 demonstration workflow script that records ONT source metadata, read-only subdivision plans, and provenance manifests outside the repository without writing or committing derived POD5 files.
floundeR 0.5.0
Added read-only Rust-backed pod5_subdivide_plan() for deterministic POD5 file-count, sample-label, elapsed-time, and read-count planning without writing derived POD5 files.
floundeR 0.4.1
Recorded upstream mocked-reader coverage for mixed-flow-cell POD5 folder aggregation and clarified that public R mixed-flow-cell tests require the future parser-backed pod5-tools reader.
Added Rust-backed pod5_verify() and pod5_file_info() wrappers that return R-native data frames while preserving the current pod5-tools fast extension/signature verification semantics and typed POD5 error conditions.
floundeR 0.2.6
Documented the no-commit policy for downloaded POD5 files and added repository ignore guardrails for local ONT open-data caches while preserving an explicit path for intentionally tiny test fixtures.
floundeR 0.2.5
Added no-network ONT Zymo fecal POD5 dataset and selected pass/fail example object helpers so documentation, downloads, and future reports share stable source metadata.
floundeR 0.2.4
Added ont_open_data_fetch() for explicit single-object ONT open-data downloads into caller-controlled cache directories with returned provenance metadata.
floundeR 0.2.3
Added ont_open_data_list() for explicit anonymous metadata listings of the selected ONT Zymo fecal POD5 S3 prefix, including an opt-in documentation example that does not download POD5 files.
floundeR 0.2.2
Added an executable offline pod5_find() example that demonstrates in-process Rust-backed folder discovery without invoking an external CLI or requiring network/downloaded POD5 data.
floundeR 0.2.1
Documented the current R CMD check compiled-code warning introduced by linking the Rust std/pod5-tools stack, including the release posture for GitHub builds and the requirement to resolve or obtain policy acceptance before Bioconductor/CRAN-facing release work.
floundeR 0.2.0
Added pod5_find() as the first curated POD5 Rust-backed R API. The function calls the ../pod5-tools discovery library in-process and returns an R data frame with POD5-containing folders, file counts, byte totals, and modification windows.
floundeR 0.1.10
Raised the Rust toolchain floor to 1.85 and moved the embedded crate to Rust edition 2024 so floundeR can depend on the current ../pod5-tools library.
floundeR 0.1.9
Recorded the POD5 discovery preflight against ../pod5-tools, confirming that the existing find_pod5_directories() library API is the intended curated source for pod5_find().
floundeR 0.1.8
Documented source-install requirements for macOS, Linux, Windows, Docker, and CI builds of the embedded Rust extension, and made CI set up Rust explicitly.
floundeR 0.1.7
Added public R wrappers for compiled Rust capability checks, typed floundeR_rust_unavailable conditions, and a downstream test skip helper.
floundeR 0.1.6
Added an internal Rust capability function callable from R, proving the extendr scaffold can return structured R data through registered native symbols.
floundeR 0.1.5
Added the initial extendr scaffold under src/rust with R package build hooks and development-container Rust tooling.
floundeR 0.1.4
Recorded the Slice 6 cross-repository Rust preflight, confirming that the first local extendr scaffold does not require adjacent changes to pod5-tools, bamana, or porkchop.
floundeR 0.1.3
Recorded the Rust-in-R architecture decision for an embedded extendr crate with curated path dependencies on the POD5, BAM/BGZF/FASTQ, Porkchop, and optional private Grammateus engine libraries.
floundeR 0.1.2
Added qc_report_card() with schema-versioned pass/warn/fail checks and documented default thresholds for sequencing-summary-derived QC evidence.
floundeR 0.1.1
Added tidy, schema-versioned QC contracts for yield over time, read length distribution, quality distribution, channel density, and barcode composition.
floundeR 0.1.0
Added qc_run_summary() as the first versioned core QC contract for nanopore run-level summaries from normalised sequencing-summary data.
floundeR 0.0.24
Reconciled the current import surface by declaring narrow namespace imports for active FASTA, FASTQ, GenBank, plotting, and ONT open-data dependencies.
Removed stale RMarkdown-era packages from the development dependency bootstrap list now that legacy vignettes are excluded from package checks.
Documented the remaining legacy %>% and BamFile exports so release-style package checks can complete without warnings.
floundeR 0.0.23
Added a release-style package check helper that builds and checks a source tarball outside the repository, avoiding diagnostics from development-only files and local check output.
Corrected source-build ignore rules so repository governance files, development scripts, .github, and .dockerignore are excluded from package tarballs.
floundeR 0.0.22
Moved legacy RMarkdown vignettes to repo-only historical reference material while executable report workflows move to the Grammateus migration.
floundeR 0.0.21
Corrected POD5 manifest fixture checksum values so they remain character SHA-256-like hex strings under package checks and schema tests.
floundeR 0.0.20
Added a small installed BLAST fixture and restored Blast$count() behavior so the BLAST example and test no longer depend on a missing large UniRef output file.
floundeR 0.0.19
Added conservative sequencing-summary column alias handling for current Dorado and MinKNOW/POD5-era summary shapes.
Allowed reduced Dorado summary files without passes_filtering to import as partial QC inputs with an explicit warning and NA logical values.
Added regression coverage for legacy Guppy-like and Dorado-like sequencing summary fixtures.
floundeR 0.0.17
Added a Docker-backed development build path and a dependency audit script for assessing declared CRAN/Bioconductor package versions and support channels in a clean container.
Recorded the current R 4.6.0/Bioconductor 3.23 dependency snapshot and the package-quality failures exposed once dependencies are available.
floundeR 0.0.16
Added fixture-backed schema tests for the initial sequencing-summary, barcode-summary, and POD5-manifest QC table contracts.
floundeR 0.0.15
Added a test helper and development guidance so optional compiled Rust-backed tests skip cleanly until in-process bindings are available.
floundeR 0.0.14
Added a test helper and development guidance that keep network-dependent ONT open-data/S3 tests opt-in through FLOUNDER_RUN_NETWORK_TESTS=true and skipped by default on CRAN-like checks.
floundeR 0.0.13
Added small offline test fixtures for sequencing summaries, barcoding summaries, FASTQ, FASTA, and POD5 metadata manifests without committing binary POD5 files.
floundeR 0.0.12
Added a dry-run-first R dependency bootstrap script and development notes for local checks after FAST5 retirement.
Configured the package for testthat edition 3.
floundeR 0.0.11
Retired the active FAST5 API surface by removing the Fast5 export, implementation, fixtures, tests, vignette, generated reference page, and rhdf5 dependency. Raw-signal QC now points toward POD5-era integration.
floundeR 0.0.10
Added a repository-level governance check that enforces the open-source boundary for floundeR, pod5-tools, bamana, and porkchop while keeping Grammateus private, optional, and distributed through prebuilt runtime assets.
floundeR 0.0.9
Added Porkchop to the curated open-source Rust engine plan for adapter, primer, barcode, kit-registry, and cDNA/library-preparation QC evidence.
floundeR 0.0.8
Documented the distribution boundary: floundeR, pod5-tools, and bamana stay open-source, while Grammateus remains private and is consumed through optional prebuilt runtime/reporting artifacts.
floundeR 0.0.7
Added an explicit Grammateus reporting interface plan for dropping R plots into governed HTML/PDF reports and for controlled R plot generation from Grammateus report specifications.
floundeR 0.0.6
Started the reboot planning baseline for contemporary nanopore QC and review.
Documented the FAST5 retirement direction, selective Rust-in-R integration with pod5-tools, bamana, and grammateus, ONT POD5 example-data policy, and synoptikon reporting ambitions.
Reconciled package metadata and declared currently referenced dependencies so package checks can progress beyond initial DESCRIPTION validation.
floundeR 0.0.5
floundeR 0.0.4
inclusion of a basic Rsamtools derived FASTA R6 class (lodestar dependency)
starting to ensure that methods are also available through documented magrittr %>% pipes for legibility of code
robust Angenieux decorations and demonstration of more comprehensive plots
integrating Angenieux with ggsave for cleaner Rmarkdown usage
floundeR 0.0.3
pkgdown documentation for the github pages
creation of angenieux prototype; code linking and POC
creation of the R6 object called FlowCell
Sequencing summary push …
simplified FAST5.is_multi_F5 logic; there were some issues with different version of the hdf5 api - tested on Windows and macOS.
floundeR 0.0.2
starting to populate content
inclusion of FAST5 parsing content, vignette and test data
floundeR 0.0.1
tagged a first version
floundeR 0.0.0.9000
Added a NEWS.md file to track changes to the package.