Core port: storage, importer, reports, CLI and desktop UI (Phases 2–7)#2
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Adds Census.Storage with a forward-only embedded-SQL migration runner (Migrator) and a Dapper-backed SqliteProjectStore (Create/Open/SaveRun/GetRuns). Schema v1 covers runs, estimations, parameters, warnings, and file_artifacts with cascade deletes and indexed foreign keys. Round-trip and idempotency tests pass on all three platforms. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Implements NonmemXmlImporter.Import() with XDocument/LINQ-to-XML parsing robust to both NONMEM 7.2 (bare element names) and 7.6+ (nm: namespace prefix) output. Extracts estimations, theta/omega/sigma parameters with standard errors and shrinkage, condition number, OFV, warnings, and ObsRecs/Individuals from problem_options. MD5 computed on source file. Fixture run27.xml covers the NONMEM 7.6 format; inline XML tests cover the 7.2 legacy etashrink fallback, termination warnings, and simulation runs. 14/14 tests pass. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Real NONMEM 7.3-7.5 output writes etashrink/etashrinksd as a single SUBPOP1 row with one col per eta, not one row per eta. ParseMatrix was only extracting shrinkage for the first eta in this format. Add FlattenShrinkageValues helper that detects the layout and returns an indexed list that ParseMatrix can use without further branching. Add a test for the flat shrinkage format and RealWorldImporterTests that validates all 276 NM 7.3/7.4/7.5/7.6 IQ reference XML files on this machine parse without exceptions and report expected field coverage. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…tWriter Adds ParameterRow (internal record struct with RSE/CI computed fields), CsvReportWriter (IReportWriter/CSV via CsvHelper, G6 invariant formatting), and 5 xUnit tests covering header, theta values, omega shrinkage, no-estimations, and null-SE edge case. All 25 tests pass. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds HtmlReportWriter (IReportWriter) that renders runs to a complete HTML5 document via an embedded Scriban template, with snapshot and assertion tests. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…chive, compare) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…d run list Replace the scaffold placeholder with a real application shell: DockPanel layout with menu, toolbar, status bar, and a DataGrid showing run summary columns (RunNo, Parent, Method, OFV, dOFV, ConditionNumber, Obs, Ind, Key, Warnings). Add IDialogService/AvaloniaDialogService for file pickers, ISettingsService/JsonSettingsService for persistent settings, AppSettings model, RunSummaryViewModel, and wire up MainWindowViewModel with commands for New/Open/Close/Exit project lifecycle. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add ImportRun, ImportFolder, ExportRun, and ArchiveRun relay commands to MainWindowViewModel with CanExecute guards, and wire toolbar buttons and File menu items in MainWindow.axaml. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds a release job that runs after all publish jobs succeed on a tag, downloads the four platform artifacts, renames them with RID suffixes, and creates a GitHub Release with auto-generated notes. Signing stubs remain as TODOs pending certificate provisioning. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Generates checksums.txt alongside binaries in each GitHub Release so users can verify downloads independently of code signing. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Replicates the classic Census interface: - Icon toolbar (New/Open Database, Import Run/Folder, Delete Run, Compare, Diagnostics, Report, Preferences, Quit) using Segoe Fluent Icons glyphs. - Left sidebar with vertical "Project Overview / Run Files" tab strip, a "Filter" header, an "All runs" navigation tree, and an Expanded toggle that selects runs and drives the grid. - Run list columns Run / Flag (status circle) / Comment / OFV / dOFV (red when non-zero) / Parent / Cond No / Warnings. - Bottom split: "Estimation" steps grid on the left driving the parameter tabs (Theta/Omega/Sigma/Matrices/Miscellaneous/PsN) on the right; selecting a step updates the parameter tables. - "Connected – <path>" status bar; Light theme variant to match the original look. Adds IProjectStore.DeleteRun (cascades via FK) and wires Delete Run, Compare and Diagnostics commands into the view model. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…PROBLEM Importer now reads per-estimation estimation_elapsed_time and covariance_elapsed_time, run-level start_datetime/stop_datetime/ total_cputime, and problem-level post_elapsed_time/finaloutput_elapsed_time. Run.Comment defaults to the $PROBLEM title (problem_title) when no PsN run name is present. Schema migration 0002 adds the timing columns; SaveRun/GetRuns persist and load them. The Estimation grid gains Est Time and Cov Time columns, and the run-level timings are appended as labelled rows. Tests: importer test for timings + problem-title comment; storage round-trip extended to cover all new fields. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- Top run grid gains Start, Stop and Total CPU columns (run-level values that apply to the whole run). - Estimation grid gains Post Time and Final Out columns (per-problem values shown on each $EST step row); the previously appended run-level timing rows are removed. - Estimation grid stays one row per $EST step; multi-$PROBLEM files remain out of scope (importer reads the first problem only). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- Grid cell and column-header font size now comes from a GridFontSize dynamic resource (default 11, one level smaller than the 12 used elsewhere). Configurable in Preferences and applied live. - Persisted via AppSettings.GridFontSize and applied at startup. - Override Fluent TabItemHeaderFontSize so bottom-right tab headings match the rest of the UI (12) instead of the oversized default. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Real NONMEM 7.3 output leaves covariance_status eigenvalues zeroed and has no <eigenvalues> element, so condition numbers were never populated. The importer now derives the condition number (ratio of largest to smallest eigenvalue of the correlation matrix) via a Jacobi eigensolver, falling back through: explicit <eigenvalues> vector, populated covariance_status, then the <correlation> matrix. Fixed parameters (zero SE) are excluded, and non-positive-definite matrices yield no value. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- Add analytical 3x3 equicorrelation case (eigenvalues 2.0, 0.5 -> cond 4.0) to validate the Jacobi solver beyond the 2x2 case. - Strengthen the real-world importer test to assert condition numbers now populate from the correlation matrix and are all positive and finite. Note: none of the 276 reference runs printed eigenvalues (PRINT=E off), so NONMEM reported no condition number to diff against; values are validated analytically and for positivity/finiteness instead. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
kestrel99
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Jun 15, 2026
PORTING_PROGRESS_REVIEW.md gap #2: the CLI/UI/API text promised "XML or listing" and PsN import, but the only importer is NonmemXmlImporter (.xml). Behaviour was already XML-only via CanImport; this aligns the promises. - IRunImporter doc: state .xml is the only format today; listing/PsN planned. - CLI: import/import-folder descriptions and the <source> argument help now say XML output, not "XML or listing". - GUI import picker: drop the misleading "All Files" filter (XML-only). - GUI ImportRun: guard with CanImport and report parse failures via status text instead of throwing unhandled. dotnet test: 60 passed, 0 failed. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
Builds out the .NET 10 / Avalonia port of Census across Phases 2–7: a clean domain model, SQLite storage, the NONMEM XML importer, report/export/archive, the CLI, the desktop UI replicating the original Census, and the release pipeline.
What's included
Domain & storage
Census.Domainrecords (Run, Estimation, Parameter, FileArtifact).0001_initial,0002_timing); cascade deletes;DeleteRun.Importer (
Census.Import)Commentfrom$PROBLEMtitle.Reports / archive / CLI
censusCLI: import, import-folder, export-run, compare, archive.Desktop UI (
Census.App, Avalonia)Release pipeline
Tests
43 xUnit tests pass (importer incl. real-file corpus, storage round-trip, condition-number eigensolver). Release build clean.
Follow-ups (not in this PR)
.lstlisting parser (if needed).🤖 Generated with Claude Code