chore(main): release 2.0.0

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2.0.0 (2026-07-09)

Release Notes

Overview

This release delivers major improvements across the public catalog, submission workflow, DOI and citation handling, ELN integrations, dashboard usability, security hardening, and platform infrastructure. It also includes a large framework upgrade, improved CI coverage, and several fixes for publishing, search, authentication, and embargo handling.

Highlights

• Expanded and updated the submission and upload workflows with a better file browser, provisional DOI reservation, processing logs, draft status handling, and clearer publishing controls. (#1396)
• Added Chemotion ELN integration. (#1370)
• Added a refreshed public site experience with shared navigation, landing page, FAQ page, updated legal pages, modern empty states, and improved public project, study, sample, and compound layouts. (#1424, #1396, #1416)
• Introduced a unified search experience with structure search, catalog text search, IUPAC name support, and improved compound browsing. (#1416, #1422)
• Segregated submission workflow into two options - Publication Deposition - to deposit spectra linked to a manuscript, preprint or thesis. Community Contribution - to contribute raw or processed spectra for open science. (#1442, #1425)
• Upgraded the platform to Laravel 13 and modernized PHP, Node, CodeQL, Docker, and CI tooling. (#1441)
• Strengthened security around authentication, user enumeration, package advisories, CSP, and API access. (#1340, #1389)
• Add job for metadata extraction and generate BagIt packages. (#1366)

Features

Public site and user experience

• Added a shared public site header, navigation utilities, deposit CTA helpers, and a dedicated FAQ page. (#1416, #1417)
• Redesigned public-facing pages including Welcome, About, FAQs, Legal, Projects, Studies, Samples, and Compounds. (#1416, #1424)
• Added reusable footer and refreshed legal page layouts. (#1352)
• Redesigned the FAQ component with updated user-focused content. (#1352)
• Added modern empty states for dashboard and public pages. (#1352)
• Added deterministic seeded cover backgrounds for projects without custom images. (#1396)
• Added “Coming Soon” indicators for unreleased search and prediction features. (#1352)
• Added “What’s New” notifications for users after each release. (#1438)

Search and discovery

• Added a unified search modal with structure search and planned support for spectra, peak list, and metadata search. (#1352)
• Added reusable structure editor components based on OpenChemLib. (#1352, #1416)
• Added catalog text search API endpoints and a public search page. (#1422, #1416)
• Added IUPAC name support to compound search. (#1396, #1445, #1352)
• Scoped compound catalog listings to molecules with public spectra. (#1396)
• Improved compound catalog pagination and default sorting. (#1396)
• Added visual assets for search cards and spectrum previews. (#1352)
• Redirected legacy /spectra routes to the new public project or compound routes. (#1396)

Submission, upload, and publishing

• Redesigned the submission primer and reused it across upload/submission flows. (#1396)
• Restored and improved the file browser layout with drag-and-drop support, resizable sidebar behavior, breadcrumbs, folder sorting, expand/collapse controls, and better scroll handling. (#1396, #1352)
• Added Magritek Spinsolve dataset support and support classic and modern Spinsolve folder layouts.
• Added provisional DOI reservation, DOI preview/copy UI, and backend endpoints for draft-level DOI reservation. (#1396)
• Added draft status handling, draft show endpoint, and better draft recovery after refresh. (#1396, #1293, #1425)
• Added processing logs in the upload and submission workflows. (#1396)
• Added support for publishing a single-sample project either as an individual sample or as a project. (#1342)
• Added sample-only publishing validation so project metadata can be skipped when publishing individual samples. (#1396)
• Added support for finalizing republish jobs when the original draft has already been removed. (#1437, #1396)
• Improved project release scheduling and embargo metadata UI. (#1396)

DOI, citations, and metadata

• Added provisional DOI storage, placeholder generation, DataCite metadata enrichment, and provisional registration tracking. (#1396)
• Made DOI optional for manual citation entry and refined DOI validation. (#1373, #1375)
• Added study-citation pivot support and end-to-end citation sync between projects, studies, samples, and ELN metadata. (#1396)
• Added citation display on public study and sample pages. (#1396, #1394)
• Improved citation attachment for ELN submissions. (#1370)
• Added metadata extraction and BagIt package generation jobs. (#1366)
• Added JCamp helpers, Bioschemas/NMRium metadata handling, and verification commands. (#1396)
• Persisted spectrum assignments on datasets. (#1396)

ELN and integration support

• Added NOBS metadata extraction support. (#1350, #1366)
• Registered NOBS as a supported ELN system in the backend factory and API. (#1350)
• Added NOBS upload UI option, logo assets, and CSP support. (#1350, #1352)
• Improved Chemotion/ELN citation association. (#1370)
• Added authenticated proxy support for chemistry standardization requests to avoid browser CORS issues. (#1396)
• Updated chemistry standardization configuration to use the current service URL. (#1350)
• Added nmrKit deployment support in development and production deployment files. (#1430)
• Migrate standardize API from cheminf.studio to api2.naturalproducts.net (#1350, #1396)

Dashboard and workspace

• Added dashboard project search, filtering, pagination, and unified project badge logic. (#1277)
• Added compound-library queries and workspace molecule statistics. (#1396)
• Improved dashboard filters and project listing UX. (#1423)
• Added member workspace context to canonical public project routes. (#1396)
• Improved dashboard sidebar navigation and workspace-aware active states. (#1396, #1352)
• Fixed owner viewer-role resolution when the owner is not present on the members pivot. (#1416, #1423)
• Added community contribution backend and UI for partial sample publishing. (#1425, #1442)

Authors and affiliations

• Added ROR integration for user and author affiliations. (#1316)
• Added study-author relationships, including pivot table support and resource serialization. (#1350)
• Displayed study authors in dashboard and public sample views. (#1350, #1394)
• Added null-safe support for studies without parent projects. (#1350, #1396)
• Improved author and citation navigation/editing flows. (#1439, #1445)

Bug Fixes

Authentication and account flows

• Fixed login validation redirects so failed login errors reliably show on /login. (#1395)
• Fixed duplicate flash prop handling that hid auth and social login error messages. (#1372)
• Improved API login responses for unverified accounts. (#1340, #1395, #1394)
• Removed unused ORCID configuration. (#1426, #1272, #1317)
• Fixed user enumeration risks across auth, password reset, invitation flows, and public API filters. (#1340)

Publishing and embargo handling

• Fixed release-date comparisons so same-day releases are handled correctly. (#1384)
• Fixed overdue embargo state handling and embargo notices. (#1415, #1401)
• Fixed release-now behavior for embargoed projects. (#1401)
• Improved embargo publication validation and error handling. (#1401, #1406)
• Fixed project publishing when drafts were already removed. (#1437, #1396)
• Fixed publish file moves and draftless submissions by preventing archive churn during filesystem rewrites. (#1396)
• Fixed species and tag updates so partial saves can clear or replace metadata intentionally. (#1396)

Upload, draft, and file browser

• Fixed draft retrieval on refresh by scoping default drafts by team and persisting draft_id at step 2. (#1371)
• Fixed cross-team draft mismatches. (#1371)
• Fixed dropzone checksum calculation for asynchronously discovered folder files. (#1396)
• Fixed project-name editor layout and folder-structure help row alignment. (#1396)
• Fixed tooltip positioning, clipping, and stacking issues. (#1396)
• Fixed main layout shrinking issues for nested scroll areas. (#1396)
• Fixed central draft creation behavior in the app sidebar. (#1421)

Search, routes, and public pages

• Fixed compound route resolution for /compound/M### identifiers. (#1390, #1340)
• Fixed compound search issues. (#1445, #1352, #1396)
• Fixed missing compound metadata during processing with repair and enrichment commands. (#1419)
• Fixed public rendering for samples/datasets without parent projects. (#1396)
• Fixed author and citation back-navigation. (#1439, #1445)
• Fixed broken sample-view and documentation links. (#1347, #1352)
• Fixed public page tests after the public Inertia refactor. (#1416, #1417)
• Fixed dashboard search loading and case-sensitive search behavior. (#1411, #1416)

API and data handling

• Fixed schema API empty-result responses. (#1437)
• Removed deprecated search endpoints and updated affected API responses. (#1437, #1416)
• Fixed invalid identifier behavior to return proper 404 responses. (#1437)
• Fixed DataController filter responses. (#1437)
• Fixed ORCID API CORS/refactoring issues. (#1317, #1284)
• Fixed CAS provider configuration and refactored CAS integration into a service.
• Fixed ROR affiliation route throttling and moved ROR API access to a controller. (#1316)

UI and frontend

• Fixed OpenChemLib imports for Vite. (#1396, #1416)
• Fixed reserved Vue component names and prop typing issues. (#1394)
• Fixed duplicate radio input values in the structure editor. (#1352)
• Fixed unused Vue refs in the prediction component. (#1352)
• Fixed TIFF project image uploads by restricting allowed image formats to JPG, PNG, GIF, and WebP. (#1340, #1391)
• Fixed sample citation placement in the public sample layout. (#1352)
• Fixed draft tag UI/UX and broken links. (#1397)
• Fixed admin email configuration. (#1407)
• Fixed publish email duplicates and template issues. (#1284)

Backup, workers, and reliability

• Hardened Postgres backup job error handling. (#1420, #1352)
• Fixed FrankenPHP worker API throttling behavior in test environments. (#1336)
• Added and corrected Docker health checks for app and worker images. (#1339)
• Fixed worker Docker PHP 8.4 image and extension installation issues. (#1329)
• Fixed package lock synchronization after dependency updates. (#1430)

Security

• Added anti-spam protection for the support bubble with reCAPTCHA v3, server-side validation, and rate limiting. (#1281)
• Hardened user enumeration protections in login, password reset, invitation, and public API flows. (#1340, #1389)
• Removed the public owner.email filter and sort options. (#1340)
• Updated package dependencies to address npm, Composer, AWS SDK, Preact, Vite, Laravel, and related security advisories. (#1314, #1340, #1425)
• Added and refined Content Security Policy sources for ORCID, NMRium, NOBS, Meilisearch, TIB Terminology Service, and configurable endpoints. (#1399, #1350)
• Restricted project image uploads to supported image formats. (#1340, #1391)
• Added authenticated and throttled chemistry standardization proxy endpoint. (#1396)
• Improved draft ownership policies and authorization checks for community contribution and publish endpoints. (#1425, #1442)

Performance and Reliability

• Added automatic skip/error handling for failed snapshot imports so batch generation continues after problematic spectra. (#1352)
• Improved molecule sanitization with fewer database writes, API retry logic, rate limiting, transactions, and better logging. (#1352)
• Added structured publish-pipeline trace logs for easier production debugging. (#1396)
• Added compound metadata repair jobs and enrichment inspectors. (#1419, #1416)
• Added queue, DOI, Horizon, trust proxy, and PHPUnit configuration updates. (#1396)
• Increased PHP memory limits for queue-heavy workloads. (#1418)
• Improved file browser reactivity by making expanded folder state updates safe in Vue 3. (#1396)

Developer Experience and Infrastructure

• Upgraded PHP usage from 8.2 to 8.4 in Docker and workflows. (#1307, #1329)
• Upgraded the application stack to Laravel 13 with compatible framework/package updates. (#1441)
• Updated Laravel 13 configuration, Sanctum CSRF middleware, cache serialization defaults, PHPUnit 12 schema, and Swagger/OpenAPI generation. (#1441)
• Added Docker smoke tests for FrankenPHP app and worker images. (#1339)
• Added test and coverage workflows, API test suite inclusion, Codecov updates, and broader automated test coverage. (#1313, #1286)
• Adopted Node 24-ready GitHub Actions and CodeQL v4. (#1394)
• Added Laravel Boost and updated Cursor/Laravel Boost guidelines. (#1352, #1441)
• Added Husky pre-commit hooks for linting, formatting, and quality checks. (#1316)
• Ignored generated Swagger UI assets. (#1340)
• Moved direct environment usage into configuration files and cleaned up .env.example. (#1281, #1353, #1350)
• Updated frontend lockfiles, Vite/OpenChemLib configuration, Composer dependencies, and npm package overrides. (#1416, #1396, #1340)

Tests

• Added and expanded tests for models, projects, studies, drafts, file system, dashboard, downloads, admin controllers, datasets, API endpoints, ROR, ORCID, services, email notifications, jobs, teams, DOI helpers, compound repair, publishing, embargo behavior, public Inertia pages, and community contribution workflows. (#1322, #1288)
• Added Docker smoke test coverage for app and worker images. (#1339, #1286)
• Improved CI reliability by fixing flaky tests, database setup issues, public Inertia assertions, and test factory defaults. (#1417, #1416)

Upgrade Notes

• This release includes a Laravel 13 upgrade. Review deployment configuration, package compatibility, PHPUnit configuration, and framework-related config changes before production rollout. (#1441)
• The application now expects the updated PHP/runtime stack used by the Docker and workflow changes, including PHP 8.4-compatible images and dependencies. (#1307, #1329)
• Legacy /spectra routing has been redirected or replaced by project and compound routes. Any external links or documentation using old spectra URLs should be reviewed. (#1396, #1352)
• Deprecated search endpoints were removed or replaced by the normalized catalog search endpoints under the new search API. (#1416, #1437, #1422)
• CSP configuration now includes additional services. Production deployments should verify environment-specific CSP sources for ORCID, NMRium, NOBS, Meilisearch, TIB, and chemistry standardization. (#1272, #1399)
• Queue-heavy processing now relies on updated Horizon, memory, and worker configuration. Check production worker and supervisor settings after deployment. (#1418, #1430)
• Project image upload validation is stricter. TIFF and unsupported formats are rejected. (#1340)

Internal Cleanup

• Removed obsolete Larabug error tracking package and related configuration. (#1340)
• Removed duplicate migrations and duplicate services. (#1350, #1307, #1382)
• Cleaned up unused ORCID configuration. (#1426, #1272, #1317)
• Reorganized tests and improved naming/structure. (#1324, #1320)
• Replaced several hardcoded URLs with named routes. (#1396)
• Reduced duplicated UI code by extracting shared public, footer, search, file browser, and dashboard components. (#1352, #1417)

Unmapped release-note items

These release-note bullets did not have a direct or confident match in the supplied original changelog:

• Features / Submission, upload, and publishing: Added Magritek Spinsolve dataset support and support classic and modern Spinsolve folder layouts.

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