v1.0.0

Added

• Bioinformatics Plugins on every menu: the thirteen built-in plugins (Eukaryotic and Microbial Gene Predictors, CRISPR Repeat Array Finder, Microsatellite & Tandem Repeats, Haplotype & Allele Partitioner, Taxonomic Sequence Classifier, Species Delimitation, Protein Domains & Epitopes, Transmembrane & Signal Topology, Adapter & Quality Read Trimmer, Whole-Genome Synteny Blocks, HPC Phylogeny Job Builder, External CLI Suite) are under Tools › Bioinformatics Plugins in the native macOS menu bar and the in-window menu bar, under the toolbar's Workflows ▾ menu, and in the search bar. Before, they were reachable only from the in-window menu, which the macOS desktop app hides. Each plugin's method is cited in PROVENANCE.md.
• Mol 3D structure viewer*: PDB and mmCIF structures render in Mol* (MIT, credited in NOTICE) with representation presets, styles, colour schemes, a sequence panel, ligands, superposed Model B and PNG export.
• Preferences that take effect: Files & Tabs › default folder for opening and saving files and default Author for new files, Export › default format for DNA, RNA, protein and alignment exports, and the other General, DNA, RNA, Protein, Gel, Trace, Enzyme, Primer and Keyboard settings are now saved, applied at once, exported to and imported from .mbcprefs.json, and restored by Reset All Preferences.
• Styled macOS disk image: the .dmg opens on a light-blue grid welcome window with the app icon, an Applications shortcut and an arrow between them, and its licence agreement is set in Google Sans.
• Align Structures… is on the menus: Tools › Alignment and the toolbar's Align dropdown, and the native Alignment menu on the desktop. It opens the structure alignment window (align two chains by structure, TM-align-style, or by sequence) and is disabled until the session holds a structure document; in the in-window menus the greyed item's hint gives the reason. It can be given a keyboard shortcut or toolbar button, and has a help topic.
• 3D Structure tab, viewer annotations: for an mmCIF structure the viewer shows the ligands bound to the chains it draws, colours by the helices and strands the file declares ("SS from file"), and highlights the residues of the selection made in the sequence view (clicking a feature selects its range). For legacy PDB text the tab says these are read from mmCIF.
• 3D Structure tab, Ramachandran plot: the open chain's backbone torsions are plotted under the viewer, naming the plotted model for an entry of several models ("model 1 of 2"). mmCIF only; for legacy PDB text the tab says why there is no plot.
• The nightly and release reference check re-checks the Ramachandran derivation: scripts/check_reference_suite.mjs runs derive_ramachandran_maps.py --check and fails when a cell of the six region maps in crates/molbiocraft-protein/src/backbone.rs, or one of their doc comments, no longer matches what the Top8000 grids derive, as NOTICE and PROVENANCE.md describe. It fetches the six grids from their pinned commit and checks their SHA-256, so it needs network access to raw.githubusercontent.com; a failed download fails the check. node scripts/check_reference_suite.mjs --only ramachandran runs that step alone, and MOLBIOCRAFT_REFERENCE_RAMA_GRIDS=DIR keeps the grids in DIR, so a later run downloads only the ones missing. The other MOLBIOCRAFT_REFERENCE_* variables replace the commands the check runs (Vitest, cargo, Python and the derivation script) and the maps it checks. The check prints each one that is set, and with none set it runs as before.
• Engine warnings appear in a shared Caution Amber note beside the result in the alignment studio and the MS digest, and a Multiple Alignment result keeps its warnings in its Notes. (US-01M6P25H)
• Export > Alignment Image > SVG, PNG or PDF saves the whole active alignment as a figure (blocks of 60 columns with a ruler, consensus row, each row's name and percent identity, the studio's default colours); an alignment too large for a canvas is refused with the limit named. (US-01M6S8C5)
• drag handles on the alignment studio's side panel and its sequence name and identity column (also moved with the arrow keys); both widths are kept across views and restarts; nothing changes until a handle is dragged. (US-01M6S7QS)
• Installers for every platform, each built on its own system: each release now offers MolBioCraft-<version>-macOS-universal.dmg (one app for Apple Silicon and Intel Macs, macOS 11 or later), MolBioCraft-<version>-Windows-x64.msi, MolBioCraft-<version>-Windows-x64-Portable.exe (runs without installing; needs the WebView2 runtime that Windows 10 and 11 include) and MolBioCraft-<version>-Linux-x86_64.deb (sudo apt install ./MolBioCraft-<version>-Linux-x86_64.deb), with SHA256SUMS.txt, NOTICE.txt and PROVENANCE.md beside them. The Tauri bundler builds each on a macOS, Windows or Ubuntu 22.04 runner, and each is checked to be the architecture it is named for before it is uploaded. Before, the release built only the macOS disk image, and its Windows and Linux files could not hold a working app. The builds are unsigned (the Mac app is ad-hoc signed), and README.md gives the first-launch steps past Gatekeeper and SmartScreen. Only a pushed v* tag publishes a release; running the workflow by hand uploads the same files as workflow artifacts. npm run package:installers now builds only the macOS universal .app and .dmg, with the Tauri bundler. (US-01M6TK7V)
• One shared inspector in every task window: Vectors, Cloning, Primers, Alignment (Pairwise and Dotplot), Tree, Chromatogram, Genomics, History/Protein and the Text tab now keep their settings in the same right-hand inspector as the Sequence view, with the same header button, Cmd/Ctrl+Alt+I, View › Panels › Inspector, resize handle and width. A window with nothing to set shows no button, and only one inspector shows at a time. Drawn on its own, outside the workbench, each studio keeps its settings where they were. (US-01M6TAW8, US-01M6TAT0, US-01M6TA1H, US-01M6TANN, US-01M6TA6T, US-01M6TAKD, US-01M6TAA4, US-01M6TAAR, US-01M6TA87, US-01M6TAZE, US-01M6TAKR, US-01M6TAZ7)
• The Flatfile tab's toolbar names the chosen record format beside its label, and its format buttons report their pressed state to assistive tools. (US-01M6TAZ7)
• A shared App test harness drives the real App, with its stores, menus and inspector, so each inspector change is proved in the running app. (US-01M6TB6G)

Changed

• Release notes come from this changelog: each GitHub Release now carries its version's section of CHANGELOG.md as its notes (scripts/release_notes.mjs), and a tag whose version has no section, or an empty one, fails before anything is published. (CR-01M704A6)
• README leads with what the app does: research tasks, studios, plugins, pipelines, preferences and file formats come first; build and engine details follow.
• Same menus on desktop and web: Cloning, Restriction Cloning, Enzymes, Features, Sequence and Tools have the same items, names and order in the native macOS menu bar (Tauri and Cocoa builds), the in-window menu bar and the toolbar dropdowns. Cloning opens with Clone Insert into Vector… and Validate Clone…; Restriction Cloning holds Find Sites, Digest into Fragments…, Agarose Digest, Ligate Fragments, Restriction Ligation, Anneal Oligos and Non-Cutters; Mutagenesis gains Point Mutation and Seamless Assembly gains Parts Cloning.
• Mol floating toolbar at the bottom*: the viewer's reset, screenshot, controls, expand, settings and selection-mode buttons sit in a horizontal bar at the bottom of the view, and their menus and the Screenshot and Settings panels open upward inside the view. Fullscreen expands within the app window, so the toolbar never falls outside it; the expand button or Esc returns to the normal view.
• npm run package:installers copies only the .dmg to release/, as the release packaging contract requires.
• The sample library's public-record samples are re-sourced: the samples PROVENANCE.md sections 4 and 5 list now come from public records, and each one that cites a record is checked against it. The twelve sample sequencing primers come from the iGEM Registry (VF2, VR and the five M13 primers, credited in NOTICE section 6) and from the NCBI T7, T3 and SP6 phage genomes that hold the five promoter primers; the three protein records, the yadF clone's coding sequence, the Taq gene and the genome records from NCBI records; and the two structure-backed proteins from RCSB PDB entries 1D66 and 1A4Y. The four yadF cloning primers are built from the BBF RFC 10 prefix and suffix and the Gateway attB1 and attB2 primer tails. The seven design primers are not re-sourced: they cite no record and are unchanged. Every alignment member is a public NCBI record (one protein is replaced by PDB 2ACT chain A, the record it names), and the alignments, trees and assembly reads are rebuilt from those records by MolBioCraft's own aligner, Neighbor-Joining and seeded read simulation. The fictitious-character alignment set and its tree are dropped. No sample keeps a Created or Modified field copied from another program's file. (US-01M6TDFV, US-01M6TGKH, US-01M6TGZ8, US-01M6TDSV)
• Sequence Split view: on a viewer canvas of 760px or more, the circle and the linear map sit side by side under one zoom (65-260%) that the header buttons, Cmd+=/-/0, View › Zoom and Cmd/Ctrl+wheel all move. Cmd+0 or the zoom readout also recentres a panned circle. Linear rows hold 30-60 bases to fit their column, and a selection made on the circle turns the linear map to its page.
• Alignment studio, two tab levels: the "Homology & Alignment Lenses" tab bar is gone. Distances, Lengths Graph, Virtual Gel, Fragments and Member Annotations (with its CSV export) open as inspector panels beside the grid; Chromatogram and QC Report are modes for contigs, traces and read lists; Dotplot mode d...