isomap-desktop 0.2.0__tar.gz

isomap_desktop-0.2.0/.coderabbit.yaml

@@ -0,0 +1,2 @@
+reviews:
+  abort_on_close: false

isomap_desktop-0.2.0/.gitattributes

@@ -0,0 +1,2 @@
+# Opt out of AI model training
+* ai-training=false

isomap_desktop-0.2.0/.github/workflows/ci.yml

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+name: CI Pipeline
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  backend-tests:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+        
+    - name: Install dependencies
+      run: uv pip install -e ".[dev]" --system
+      
+    - name: Run pytest
+      run: pytest tests/
+    
+  ui-build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up Node
+      uses: actions/setup-node@v4
+      with:
+        node-version: 22
+        
+    - name: Install dependencies
+      working-directory: ./ui
+      run: npm install
+      
+    - name: Build UI
+      working-directory: ./ui
+      run: npm run build
+      
+    - name: Install Playwright Browsers
+      working-directory: ./ui
+      run: npx playwright install --with-deps chromium
+      
+    - name: Run E2E tests
+      working-directory: ./ui
+      run: npx playwright test

isomap_desktop-0.2.0/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+permissions:
+  contents: write
+
+jobs:
+  # ── Build Python wheel ──────────────────────────────────────────────────
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Build distribution
+        run: |
+          pip install build
+          python -m build
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  # ── Publish to PyPI ─────────────────────────────────────────────────────
+  publish-pypi:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/
+          skip-existing: true
+
+  # ── GitHub Release ─────────────────────────────────────────────────────
+  create-release:
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          name: IsoMap ${{ github.ref_name }}
+          generate_release_notes: true
+          files: |
+            dist/*.whl
+            dist/*.tar.gz
+          fail_on_unmatched_files: false
+
+  # ── Build Tauri Apps ─────────────────────────────────────────────────────
+  build-tauri:
+    needs: create-release
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - platform: 'macos-latest'
+            args: ''
+          - platform: 'ubuntu-22.04'
+            args: ''
+          - platform: 'windows-latest'
+            args: ''
+    runs-on: ${{ matrix.platform }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+
+      - name: install Rust stable
+        uses: dtolnay/rust-toolchain@stable
+        
+      - name: setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: install dependencies (ubuntu only)
+        if: matrix.platform == 'ubuntu-22.04'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgtk-3-dev libwebkit2gtk-4.1-dev libappindicator3-dev librsvg2-dev patchelf
+
+      - name: install frontend dependencies
+        working-directory: ui
+        run: npm install
+
+      - name: build python sidecar
+        shell: bash
+        run: |
+          pip install -e ".[dev]"
+          ./scripts/build-sidecar.sh
+
+      - name: build tauri app
+        uses: tauri-apps/tauri-action@v0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tagName: ${{ github.ref_name }}
+          releaseName: 'IsoMap ${{ github.ref_name }}'
+          releaseDraft: false
+          prerelease: false
+          args: ${{ matrix.args }}

isomap_desktop-0.2.0/.gitignore

@@ -0,0 +1,84 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Environment
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Virtual Environments
+.virtualenv
+
+# React/Node
+node_modules/
+.npm
+ui/dist/
+ui/node_modules/
+ui/.env.local
+ui/.env.development.local
+ui/.env.test.local
+ui/.env.production.local
+
+# IDEs
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# MacOS
+.DS_Store
+
+# Logs
+*.log
+
+# SQLite databases
+*.sqlite
+*.sqlite3
+*.db
+!data/taxonomy/*.db
+
+# Tauri
+ui/src-tauri/target/
+# Machine Learning Modelsassets/models/
+
+# Machine Learning Models
+assets/models/
+# AI agent / framework config (personal development environment)
+.aidevops.json
+AGENTS.md
+CLAUDE.md
+TODO.md
+.agents/
+.claude/
+todo/
+
+# IDE / editor files
+.windsurf/
+.ctx/
+.beads/
+.gitnexus/

isomap_desktop-0.2.0/.gitlab-ci.yml

@@ -0,0 +1,10 @@
+stages:
+  - verify
+
+verify-job:
+  stage: verify
+  script:
+    - echo "Repository is clean."
+  only:
+    - main
+    - master

isomap_desktop-0.2.0/.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.2
+    hooks:
+    -   id: ruff
+        args: [ --fix ]
+    -   id: ruff-format

isomap_desktop-0.2.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to IsoMap are documented in this file.
+
+## [0.2.1] — 2026-06-12
+
+### Fixed
+- **CI/CD**: Resolved PyInstaller pathing failures for Windows runners to successfully produce native Windows desktop installers via GitHub Actions.
+
+## [0.2.0] — 2026-06-11
+
+### Added
+- **Tauri v2 desktop application**: Full Rust backend with 9 JSON-RPC bridge commands (`import_dataset`, `get_sheet_names`, `map_columns`, `save_override`, `get_spatial_preview`, `normalise_chronology`, `validate_dataset`, `export_dataset`, `generate_data_paper`)
+- **Connected wizard flow**: Import → Column Mapping → Chronology → Spatial → Validation → Export pipeline with shared state across all 6 wizard tabs
+- **StatusBanner component**: Animated CSS spinner, color-coded loading/error/empty/success banners, Retry buttons on all components
+- **E2E test suite**: 6 Playwright tests with in-browser mock Tauri bridge (`mockTauri.ts`), covering full wizard flow
+- **3 new repository schemas**: `pangaea.json` (20 fields), `noaa.json` (24 fields), `lipd.json` (24 fields) — total 5 supported repositories
+- **Cross-platform sidecar scripts**: macOS (Intel + Apple Silicon) and Windows batch wrappers
+- **PyInstaller packaging**: `scripts/isomap-sidecar.spec` and `scripts/build-sidecar.sh` for standalone binary distribution
+
+### Changed
+- **Schema path resolution**: data/schemas and preferences.db now resolve relative to `__file__`, not CWD — works regardless of Tauri bundle location
+- **ColumnMapper**: added schema selector dropdown with all 5 repository options
+- **ImportWizard**: fires `onImportComplete` callback to feed shared wizard state
+- **Downstream tabs**: disabled until a file is imported via the Import Engine
+
+### Fixed
+- **Rust/Python IPC**: Fixed JSON-RPC Serde deserialization conflicts (camelCase vs snake_case) and Python `sys.exit()` codes causing Rust to fail parsing errors.
+- **Python Backend**: Corrected Valentine matcher API structure, stabilized validation JSON serialization to prevent crashes on timestamps/numpy types, fixed `bce` regex matching, and corrected SQLite queries in preferences.
+- **Frontend React**: Resolved infinite re-fetch loops in ValidationReport by stabilizing JSON string keys, optimized `chronologyMappings` with `useMemo`, and added robust loading guards against concurrent dataset operations.
+- **Security/Config**: Set secure CSP headers in `tauri.conf.json` and removed overly broad `shell:allow-execute` capabilities.
+- CI: removed broken uv cache glob, bumped Python 3.10→3.12, Node 18→22
+- CI: Playwright port mismatch (5173→1420), VITE_E2E=true for mock Tauri in tests
+- `xlsxwriter` dependency missing from pyproject.toml (NOAA export)
+- ONNX model graceful skip when `assets/models/` is absent (CI)
+- Unused `React` import in ErrorBoundary (React 19 auto-JSX)
+- Hardcoded column name mismatches in App.tsx test fixtures
+
+## [0.1.0] — 2026-06-06
+
+- Initial release with GitHub Release workflow and PyPI publishing
+- Python wheel (`isomap-0.1.0-py3-none-any.whl`) and source tarball artifacts
+
+## [Pre-release] — 2026-05-29
+
+### v3.0 Features
+- PANGAEA tab-delimited export template
+- NOAA NCEI Paleoclimatology Excel template
+- SciBERT ONNX quantised model for semantic column matching
+- ESSD-compliant LaTeX data paper generation (Jinja2)
+
+### v2.1 Features
+- Valentine Ensemble Matching (Coma & Cupid structural schema matching)
+- Semantic Web RO-Crate export (Frictionless Data + provenance)
+
+### v2.0 Features
+- PyLiPD native Linked Paleo Data export
+
+### v1.0 Features
+- **Import Engine**: CSV and Excel (.xlsx, .xls) with encoding detection and type inference
+- **Column Mapping Engine**: 6-stage fallback pipeline (exact → cache → fuzzy → embeddings → distribution → Valentine)
+- **Chronology Engine**: `cal_BP` normalisation with 1950 CE anchor
+- **Spatial Verification Engine**: GeoDataFrame coordinate cleaning and bounding box export
+- **Validation Engine**: Pandera constraint checking with row-level error tracking
+- **Export Engine**: CSV, Excel, GeoJSON (Neotoma), JSON (IsoArcH), LiPD, PANGAEA, NOAA, RO-Crate
+- **Provenance Engine**: PROV-O traceability metadata

isomap_desktop-0.2.0/PKG-INFO

@@ -0,0 +1,135 @@
+Metadata-Version: 2.4
+Name: isomap-desktop
+Version: 0.2.0
+Summary: Isotopic and paleoecological data standardisation middleware
+Requires-Python: >=3.12
+Requires-Dist: chardet>=5.2
+Requires-Dist: geopandas>=1.0
+Requires-Dist: httpx>=0.27
+Requires-Dist: jinja2>=3.1
+Requires-Dist: onnxruntime>=1.19
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: optimum[onnxruntime]>=1.20
+Requires-Dist: pandas>=2.2
+Requires-Dist: pandera>=0.20
+Requires-Dist: pydantic>=2.8
+Requires-Dist: pylipd>=1.3
+Requires-Dist: pyproj>=3.6
+Requires-Dist: rapidfuzz>=3.9
+Requires-Dist: rocrate>=0.15
+Requires-Dist: shapely>=2.0
+Requires-Dist: transformers>=4.40
+Requires-Dist: valentine>=1.0
+Requires-Dist: xlrd>=2.0
+Requires-Dist: xlsxwriter>=3.2
+Provides-Extra: dev
+Requires-Dist: pre-commit>=3.8; extra == 'dev'
+Requires-Dist: pytest-asyncio>=0.24; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.6; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# IsoMap
+
+Isotopic and paleoecological data standardisation middleware.
+
+IsoMap is an open-source desktop application that automates the standardisation, validation, and export of legacy isotopic and paleoecological datasets for submission to centralised repositories (Neotoma, IsoArcH, PANGAEA, NOAA NCEI, LiPD).
+
+📖 **[User Guide](USER_GUIDE.md)** — full walkthrough with screenshots, workflow steps, and troubleshooting.
+📋 **[Changelog](CHANGELOG.md)** — version history and release notes.
+
+## Features
+
+IsoMap provides a 6-tab wizard interface backed by 8 processing engines:
+
+- **Import Engine**: CSV and Excel spreadsheets with automatic encoding detection and type inference.
+- **Column Mapping Engine**: 6-stage fallback pipeline (exact → preferences → fuzzy → semantic embeddings → Valentine ensemble → distribution profiling) to accurately map source columns to 5 target repository schemas.
+- **Chronology Engine**: Auto-detects and normalises uncalibrated/calibrated dates to `cal_BP` with 1950 CE anchor.
+- **Spatial Verification Engine**: Cleans coordinates, displays on interactive Leaflet map, exports bounding box.
+- **Validation Engine**: Pandera constraint checking with row-level error tracking against schema definitions.
+- **Export Engine**: 9 output formats — CSV, Excel, GeoJSON (Neotoma), IsoArcH JSON, LiPD, PANGAEA, NOAA NCEI, RO-Crate, LaTeX data paper.
+- **Provenance Engine**: PROV-O traceability for reproducible data lineage.
+- **Automated Data Papers**: Jinja2 ESSD-compliant LaTeX manuscript generation.
+
+## Technology Stack
+
+| Layer | Technology |
+|-------|-----------|
+| Desktop shell | Tauri v2 (Rust) |
+| Frontend | React 19, Vite 7, TypeScript, Leaflet |
+| Backend (sidecar) | Python 3.12+, Pandas, Pandera, GeoPandas |
+| ML/NLP | SciBERT ONNX (Optimum), RapidFuzz, Valentine |
+| Testing | Pytest (backend), Playwright (E2E) |
+
+## Getting Started
+
+### Prerequisites
+
+- **Rust 1.70+** — [rustup.rs](https://rustup.rs)
+- **Python 3.12+** — `pip install -e ".[dev]"`
+- **Node.js 20+** with npm
+
+### Development
+
+```bash
+cd ui && npm install        # Frontend dependencies
+npm run tauri dev           # Full desktop app with hot-reload
+npm run dev                 # Vite frontend only (no Tauri)
+cd src-tauri && cargo build # Rust backend only
+```
+
+### Testing
+
+```bash
+pytest tests/               # Python backend (36 tests)
+cd ui && npx playwright test # E2E browser tests (6 tests)
+```
+
+### Production Build
+
+```bash
+./scripts/build-sidecar.sh  # PyInstaller standalone binary
+cd ui && npm run tauri build # Full desktop app bundle
+```
+
+Bundles output to `ui/src-tauri/target/release/bundle/`.
+
+## Supported Repositories
+
+| Schema | Repository | Fields | Required Fields |
+|--------|-----------|--------|----------------|
+| `neotoma_v2` | Neotoma | 11 | SiteName, Latitude, Longitude, TaxonName, Value |
+| `isoarch_v1` | IsoArcH | 10 | site_name, latitude, longitude, sample_id, material, d13c |
+| `pangaea` | PANGAEA | 20 | Event, Latitude, Longitude, Parameter, Value, Unit |
+| `noaa` | NOAA NCEI | 24 | SiteName, Latitude, Longitude, Proxy, Proxy_Value, Proxy_Unit |
+| `lipd` | LiPD v1.3 | 24 | dataSetName, SiteName, Latitude, Longitude, PaleoData_VariableName, PaleoData_Value, PaleoData_Unit |
+
+Add custom schemas in `data/schemas/` following the [JSON Schema](https://json-schema.org/) format.
+
+## Architecture
+
+```
+React invoke() → Rust Tauri commands → sidecar_rpc() → shell wrapper → Python JSON-RPC
+```
+
+The Rust layer (`ui/src-tauri/src/lib.rs`) exposes 9 Tauri commands that serialise
+parameters to JSON-RPC and forward them to the Python sidecar (`src/isomap/main.py`)
+via stdin/stdout. The sidecar processes the request and returns a JSON-RPC response.
+
+### Key Files
+
+| File | Purpose |
+|------|---------|
+| `ui/src-tauri/src/lib.rs` | 9 Tauri commands + `sidecar_rpc()` JSON-RPC helper |
+| `ui/src-tauri/tauri.conf.json` | App config, window, sidecar external binary |
+| `ui/src-tauri/binaries/isomap-sidecar*` | Platform-specific sidecar wrappers |
+| `src/isomap/main.py` | Python JSON-RPC server (stdin/stdout or CLI mode) |
+| `ui/src/api/sidecar.ts` | Frontend API layer (`invoke()` calls) |
+| `ui/src/App.tsx` | Main React app with shared wizard state |
+| `data/schemas/*.json` | Repository schema definitions |
+| `scripts/build-sidecar.sh` | PyInstaller sidecar binary builder |
+
+## License
+
+MIT
+

isomap_desktop-0.2.0/README.md

@@ -0,0 +1,104 @@
+# IsoMap
+
+Isotopic and paleoecological data standardisation middleware.
+
+IsoMap is an open-source desktop application that automates the standardisation, validation, and export of legacy isotopic and paleoecological datasets for submission to centralised repositories (Neotoma, IsoArcH, PANGAEA, NOAA NCEI, LiPD).
+
+📖 **[User Guide](USER_GUIDE.md)** — full walkthrough with screenshots, workflow steps, and troubleshooting.
+📋 **[Changelog](CHANGELOG.md)** — version history and release notes.
+
+## Features
+
+IsoMap provides a 6-tab wizard interface backed by 8 processing engines:
+
+- **Import Engine**: CSV and Excel spreadsheets with automatic encoding detection and type inference.
+- **Column Mapping Engine**: 6-stage fallback pipeline (exact → preferences → fuzzy → semantic embeddings → Valentine ensemble → distribution profiling) to accurately map source columns to 5 target repository schemas.
+- **Chronology Engine**: Auto-detects and normalises uncalibrated/calibrated dates to `cal_BP` with 1950 CE anchor.
+- **Spatial Verification Engine**: Cleans coordinates, displays on interactive Leaflet map, exports bounding box.
+- **Validation Engine**: Pandera constraint checking with row-level error tracking against schema definitions.
+- **Export Engine**: 9 output formats — CSV, Excel, GeoJSON (Neotoma), IsoArcH JSON, LiPD, PANGAEA, NOAA NCEI, RO-Crate, LaTeX data paper.
+- **Provenance Engine**: PROV-O traceability for reproducible data lineage.
+- **Automated Data Papers**: Jinja2 ESSD-compliant LaTeX manuscript generation.
+
+## Technology Stack
+
+| Layer | Technology |
+|-------|-----------|
+| Desktop shell | Tauri v2 (Rust) |
+| Frontend | React 19, Vite 7, TypeScript, Leaflet |
+| Backend (sidecar) | Python 3.12+, Pandas, Pandera, GeoPandas |
+| ML/NLP | SciBERT ONNX (Optimum), RapidFuzz, Valentine |
+| Testing | Pytest (backend), Playwright (E2E) |
+
+## Getting Started
+
+### Prerequisites
+
+- **Rust 1.70+** — [rustup.rs](https://rustup.rs)
+- **Python 3.12+** — `pip install -e ".[dev]"`
+- **Node.js 20+** with npm
+
+### Development
+
+```bash
+cd ui && npm install        # Frontend dependencies
+npm run tauri dev           # Full desktop app with hot-reload
+npm run dev                 # Vite frontend only (no Tauri)
+cd src-tauri && cargo build # Rust backend only
+```
+
+### Testing
+
+```bash
+pytest tests/               # Python backend (36 tests)
+cd ui && npx playwright test # E2E browser tests (6 tests)
+```
+
+### Production Build
+
+```bash
+./scripts/build-sidecar.sh  # PyInstaller standalone binary
+cd ui && npm run tauri build # Full desktop app bundle
+```
+
+Bundles output to `ui/src-tauri/target/release/bundle/`.
+
+## Supported Repositories
+
+| Schema | Repository | Fields | Required Fields |
+|--------|-----------|--------|----------------|
+| `neotoma_v2` | Neotoma | 11 | SiteName, Latitude, Longitude, TaxonName, Value |
+| `isoarch_v1` | IsoArcH | 10 | site_name, latitude, longitude, sample_id, material, d13c |
+| `pangaea` | PANGAEA | 20 | Event, Latitude, Longitude, Parameter, Value, Unit |
+| `noaa` | NOAA NCEI | 24 | SiteName, Latitude, Longitude, Proxy, Proxy_Value, Proxy_Unit |
+| `lipd` | LiPD v1.3 | 24 | dataSetName, SiteName, Latitude, Longitude, PaleoData_VariableName, PaleoData_Value, PaleoData_Unit |
+
+Add custom schemas in `data/schemas/` following the [JSON Schema](https://json-schema.org/) format.
+
+## Architecture
+
+```
+React invoke() → Rust Tauri commands → sidecar_rpc() → shell wrapper → Python JSON-RPC
+```
+
+The Rust layer (`ui/src-tauri/src/lib.rs`) exposes 9 Tauri commands that serialise
+parameters to JSON-RPC and forward them to the Python sidecar (`src/isomap/main.py`)
+via stdin/stdout. The sidecar processes the request and returns a JSON-RPC response.
+
+### Key Files
+
+| File | Purpose |
+|------|---------|
+| `ui/src-tauri/src/lib.rs` | 9 Tauri commands + `sidecar_rpc()` JSON-RPC helper |
+| `ui/src-tauri/tauri.conf.json` | App config, window, sidecar external binary |
+| `ui/src-tauri/binaries/isomap-sidecar*` | Platform-specific sidecar wrappers |
+| `src/isomap/main.py` | Python JSON-RPC server (stdin/stdout or CLI mode) |
+| `ui/src/api/sidecar.ts` | Frontend API layer (`invoke()` calls) |
+| `ui/src/App.tsx` | Main React app with shared wizard state |
+| `data/schemas/*.json` | Repository schema definitions |
+| `scripts/build-sidecar.sh` | PyInstaller sidecar binary builder |
+
+## License
+
+MIT
+