release: version 0.3.0

.github/workflows/ci.yml

@@ -9,4 +9,25 @@ name: CI
 
 jobs:
   test:
-    uses: MorePET/github-actions/.github/workflows/ci-python-reusable.yml@main
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install Typst
+        uses: typst-community/setup-typst@v3
+        with:
+          typst-version: 'latest'
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      - name: Run tests
+        run: make test

CHANGELOG.md

@@ -5,7 +5,7 @@ All notable changes to this template will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [0.3.0]
 
 ### Added
 
@@ -64,6 +64,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Consolidated diagram outputs to project-specific build directories
   - Simplified gitignore patterns for build artifacts
   - Updated all include paths to reference build directories
+  - Unified example and main build processes to use same pipeline (colors → diagrams → pdf → html)
+  - Example project outputs now in dedicated `example/build/` folder
 
 - **Documentation Migration**
   - Migrated all documentation from Markdown to Typst format
@@ -76,6 +78,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - TOC sidebar uses Bootstrap Offcanvas component for better mobile support
   - Improved regex patterns for SVG injection to prevent content deletion
 
+- **Typst Library Enhancements**
+  - Isotope and beta particle notation now uses Unicode superscripts/subscripts in HTML export
+  - Better accessibility with native Unicode text instead of SVG fragments
+  - Smaller HTML file sizes with improved text selection and copy/paste support
+  - PDF export unchanged (still uses physica package for proper typesetting)
+
 ### Fixed
 
 - **Table Column Widths**

Makefile

@@ -15,7 +15,7 @@ THEME_TOGGLE ?= yes
 TECH_DOC_SRC = docs/main.typ
 TECH_DOC_OUT = build/technical-documentation
 EXAMPLE_SRC = example/docs/main.typ
-EXAMPLE_OUT = example/build/example-documentation
+EXAMPLE_OUT = example/build/technical-documentation
 
 # Default target - builds the technical-documentation project
 all: technical-documentation
@@ -48,17 +48,15 @@ technical-documentation:
 	@$(MAKE) build-summary OUT=$(TECH_DOC_OUT)
 	@echo "🌓 Toggle dark mode with the button in top-right"
 
-# Build example project (depends on python-project artifacts)
+# Build example project (uses same build process as technical-documentation)
 example:
 	@echo "=================================================="
 	@echo "🎨 Building Example Project"
 	@echo "=================================================="
-	@$(MAKE) python-api
-	@$(MAKE) python-tests
-	@$(MAKE) python-diagrams
 	@$(MAKE) build-project SRC=$(EXAMPLE_SRC) OUT=$(EXAMPLE_OUT) PROJECT=example
 	@$(MAKE) server-start
 	@$(MAKE) build-summary OUT=$(EXAMPLE_OUT)
+	@echo "🌓 Toggle dark mode with the button in top-right"
 
 # Generate color files (CSS and Typst) from colors.json
 colors:
@@ -132,10 +130,10 @@ check:
 
 # Internal: Check that build outputs exist
 check-outputs:
-	@test -f technical-documentation/build/technical-documentation.pdf && echo "✓ Technical doc PDF exists" || echo "❌ Technical doc PDF missing"
-	@test -f technical-documentation/build/technical-documentation.html && echo "✓ Technical doc HTML exists" || echo "❌ Technical doc HTML missing"
-	@test -f example/build/example-documentation.pdf && echo "✓ Example PDF exists" || echo "❌ Example PDF missing"
-	@test -f example/build/example-documentation.html && echo "✓ Example HTML exists" || echo "❌ Example HTML missing"
+	@test -f build/technical-documentation.pdf && echo "✓ Technical doc PDF exists" || echo "❌ Technical doc PDF missing"
+	@test -f build/technical-documentation.html && echo "✓ Technical doc HTML exists" || echo "❌ Technical doc HTML missing"
+	@test -f example/build/technical-documentation.pdf && echo "✓ Example PDF exists" || echo "❌ Example PDF missing"
+	@test -f example/build/technical-documentation.html && echo "✓ Example HTML exists" || echo "❌ Example HTML missing"
 	@test -f lib/generated/colors.css && echo "✓ Colors generated" || echo "❌ Colors missing"
 
 # Quick test - compile everything and check outputs exist
@@ -146,7 +144,7 @@ test: technical-documentation example
 
 # Internal: Remove PDF and HTML outputs
 clean-outputs:
-	@rm -rf technical-documentation/build/
+	@rm -rf build/
 	@rm -rf example/build/
 	@rm -rf example/python-project/build/
 	@rm -f *_temp*.html

docs/main.typ

@@ -51,7 +51,7 @@
 #strong[Intended Purpose] \
 The DUPLET / EXOPET system is intended to perform simultaneous
 dual-tracer Positron Emission Tomography (PET) imaging using
-radiopharmaceuticals that emit β⁺ particles, enabling non-invasive in
+radiopharmaceuticals that emit #betaplus particles, enabling non-invasive in
 vivo detection, spatial localization, and functional characterization of
 cancer lesions with high spatial and temporal resolution. It aims to
 improve diagnosis and therapy planning by resolving intralesional and
@@ -89,8 +89,8 @@ analyzing #strong[list-mode PET data];, enabling:
 - Capture of full photon energy and timestamp data for each detection
   event.
 - Identification of #strong[triplet events];: two 511 keV annihilation
-  photons and an additional prompt nuclear gamma (e.g., from 68Ga or
-  44Sc decay).
+  photons and an additional prompt nuclear gamma (e.g., from #Ga68 or
+  #Sc44 decay).
 - Separation of signals from multiple tracers in one scan by applying
   #strong[energy-time discrimination];, positron lifetime analysis, and
   ML-supported pattern recognition.
@@ -117,15 +117,15 @@ analyzing #strong[list-mode PET data];, enabling:
     algorithms using MVA/BDT, supervised learning, and domain-adapted
     image reconstruction (CASTOR, STIR, Geant4/GATE).],
     [Radiotracers and Isotopes], [Dual-tracer combinations, typically
-    \[18F\]-FDG and \[68Ga\]-PSMA or \[44Sc\]-FAPI.],
+    #FDG and #Ga68PSMA or #Sc44FAPI().],
     [Image Analysis Workstation], [GPU-supported server platform
     integrated with BioMedIT/Leonhard Med.],
     table.hline(),
   )
 ==== Accessories
 <accessories>
 - Phantom sets for validation and calibration
-- Cyclotron-based isotope production (e.g., \[44Sc\] via Ca(p,n)Sc)
+- Cyclotron-based isotope production (e.g., #Sc44 via Ca(p,n)Sc)
 - Dose calibrators, gamma spectrometers, and QA tools
 - Clinical interface (graphical front-end for acquisition and
   processing)
@@ -314,7 +314,7 @@ analyzing #strong[list-mode PET data];, enabling:
     oncology to bridge human and veterinary diagnostics.],
     [Radiopharmacists / Radiochemists], [Experts responsible for the
     production, radiolabeling, quality control, and dosing of PET
-    tracers such as \[¹⁸F\]FDG and \[⁴⁴Sc\]-FAPI-04 under GMP or
+    tracers such as #FDG and #Sc44FAPI04 under GMP or
     equivalent standards.],
     [Software Developers / Data Scientists], [Personnel developing and
     maintaining the reconstruction, dual-tracer separation, and ML
@@ -449,53 +449,50 @@ analyzing #strong[list-mode PET data];, enabling:
   table.hline(),
   )
 
-===== Systemkomponentenübersicht – DUPLET / EXOPET
-<systemkomponentenübersicht-duplet-exopet>
+===== System Components Overview – DUPLET / EXOPET
+<system-components-overview-duplet-exopet>
 #table(
     columns: (5cm, auto),
     align: (left,auto,),
     table.hline(),
-    [Systemkomponente], [Definition und Zweck],
+    [System Component], [Definition and Purpose],
     table.hline(),
-    [PET-Detektorhardware (EXOPET-Ring)], [Modularer Ring aus
-    LYSO-Kristallen und SiPMs zur Detektion von β⁺-Annihilations- und
-    nuklearen Gammastrahlen (z. B. von ⁶⁸Ga oder ⁴⁴Sc). Ermöglicht
-    simultane Multi-Tracer-Bildgebung mit hoher räumlicher und
-    zeitlicher Auflösung.],
-    [Akquisitionselektronik & DAQ-System], [FPGA-basierte Zeitstempelung
-    und Digitalisierung aller Detektionsereignisse im List-Mode (inkl.
-    Energie & Zeit). Hohe Datenrate und Echtzeit-Speicherung zur
-    ML-gestützten Ereignisanalyse.],
-    [Bildverarbeitungssoftware & ML-Pipeline], [Software-Framework zur
-    Tracer-Diskriminierung (z. B. ⁶⁸Ga vs.~¹⁸F), basierend auf
-    Zeit-Energie-Korrelationen und ML-Algorithmen. Unterstützt
-    quantitative Bildrekonstruktion (z. B. SUV-Berechnung) und
-    Positronen-Lifetime-Analyse.],
-    [Benutzeroberfläche & Workflow-Software], [Touchscreen-gesteuerte
-    Bedienoberfläche zur Steuerung von Injektionen, Start/Stop des
-    Scans, Logging, Patientensicherheit und Positionierung.
-    Workflowführung zur Sicherstellung von Dual-Tracer-Kompatibilität.],
-    [Radiopharmazeutische Schnittstelle], [Eingabemodule für
-    Tracerinformationen (z. B. Aktivität, Injektionszeitpunkt,
-    Halbwertszeit), automatisierte Zerfallskorrektur und Verknüpfung mit
-    Dosimetriealgorithmen. GMP-konform.],
-    [Gehäuse & Mechanik], [Clamp-On-Ringstruktur zur Nachrüstung
-    bestehender PET/CT-Geräte. Wartungsfreundliches, modulares Design
-    mit Schnellzugriff auf Komponenten für Servicezwecke.],
-    [Datenexport & PACS-Integration], [HL7- und DICOM-kompatibler Export
-    an klinische IT-Systeme (PACS/RIS). Absicherung der Datenübertragung
-    durch AES-Verschlüsselung, Audit-Trail und BioMedIT-Anbindung.],
-    [Kalibrierung & QA-Zubehör], [NEMA-NU2-konforme Phantome (z. B. IEC
-    Body Phantom), automatische Kalibrierungsroutinen,
-    Tageskontrollfunktionen für Energie, Zeitauflösung und
-    Sensitivität.],
-    [Tierbildgebungsschnittstelle], [Spezielle Aufnahmeeinsätze und
-    Immobilisierungshilfen zur PET/CT-Diagnostik bei Hunden (z. B. für
-    komparative Onkologie). Anpassbar für Kleintiere.],
-    [IT-Sicherheit & Datenmanagement], [Sichere Speicherung und
-    Verarbeitung von Rohdaten und Patientendaten. DSGVO/HFG-konforme
-    Pseudonymisierung, rollenbasiertes Benutzer-Login, Datenübertragung
-    über BioMedIT/Leonhard Med.],
+    [PET Detector Hardware (EXOPET Ring)], [Modular ring of LYSO
+    crystals and SiPMs for detection of #betaplus annihilation and nuclear
+    gamma rays (e.g., from #Ga68 or #Sc44). Enables simultaneous
+    multi-tracer imaging with high spatial and temporal resolution.],
+    [Acquisition Electronics & DAQ System], [FPGA-based timestamping and
+    digitization of all detection events in list mode (incl. energy &
+    time). High data rate and real-time storage for ML-supported event
+    analysis.],
+    [Image Processing Software & ML Pipeline], [Software framework for
+    tracer discrimination (e.g., #Ga68 vs.~#F18), based on time-energy
+    correlations and ML algorithms. Supports quantitative image
+    reconstruction (e.g., SUV calculation) and positron lifetime
+    analysis.],
+    [User Interface & Workflow Software], [Touchscreen-controlled
+    interface for managing injections, scan start/stop, logging, patient
+    safety, and positioning. Workflow guidance to ensure dual-tracer
+    compatibility.],
+    [Radiopharmaceutical Interface], [Input modules for tracer
+    information (e.g., activity, injection time, half-life), automated
+    decay correction, and integration with dosimetry algorithms.
+    GMP-compliant.],
+    [Housing & Mechanics], [Clamp-on ring structure for retrofitting
+    existing PET/CT devices. Maintenance-friendly, modular design with
+    quick access to components for service purposes.],
+    [Data Export & PACS Integration], [HL7 and DICOM-compatible export
+    to clinical IT systems (PACS/RIS). Data transmission secured through
+    AES encryption, audit trail, and BioMedIT integration.],
+    [Calibration & QA Accessories], [NEMA NU-2 compliant phantoms (e.g.,
+    IEC Body Phantom), automatic calibration routines, daily quality
+    control functions for energy, time resolution, and sensitivity.],
+    [Animal Imaging Interface], [Special imaging inserts and
+    immobilization aids for PET/CT diagnostics in dogs (e.g., for
+    comparative oncology). Adaptable for small animals.],
+    [IT Security & Data Management], [Secure storage and processing of
+    raw data and patient data. GDPR/HFG-compliant pseudonymization,
+    role-based user login, data transmission via BioMedIT/Leonhard Med.],
     table.hline(),
   )
 === Verification and Validation (V&V)