Merge dev into main: sync accumulated development work (v0.0.4a)

.ai/coding-workspace.md

@@ -0,0 +1 @@
+/Users/tonyyan/Documents/GitHub/ai-common/coding-workspace.md

.ai/memory/MEMORY.md

@@ -0,0 +1,6 @@
+# Memory Index
+
+See `.ai/coding-workspace.md` for what belongs here vs `.ai/sessions/`.
+
+- [Ask before commit](feedback_ask_before_commit.md) — never `git commit` without asking first, even after verifying a fix works
+- [Preferred address](user_preferred_address.md) — address the user as "🎓Tony"

.ai/memory/feedback_ask_before_commit.md

@@ -0,0 +1,15 @@
+---
+name: feedback-ask-before-commit
+description: "Always ask before running git commit, even when changes are verified and ready"
+metadata: 
+  node_type: memory
+  type: feedback
+  originSessionId: 83fa924c-d904-40df-ba15-ec9696cf8992
+  modified: 2026-08-17T11:04:40.505Z
+---
+
+Never run `git commit` without asking Tony first, even after a fix has been implemented, tested, and verified. Staging, diffing, and reviewing changes (`git add`, `git status`, `git diff`) is fine without asking — only the commit itself requires explicit go-ahead each time.
+
+**Why:** Tony wants a final checkpoint before changes become permanent history, regardless of how confident the work is. This applies even in auto-mode / when otherwise encouraged to act without stopping for clarification.
+
+**How to apply:** After finishing and verifying a change, present the diff/summary and ask whether to commit, rather than committing and reporting after the fact. This is now codified in `.ai/coding-workspace.md` (symlinked from `ai-common/coding-workspace.md`), so it applies across all of Tony's repos, not just this one.

.ai/memory/user_preferred_address.md

@@ -0,0 +1,11 @@
+---
+name: user-preferred-address
+description: "Tony wants to be addressed as \"🎓Tony\" in conversation"
+metadata: 
+  node_type: memory
+  type: user
+  originSessionId: 83fa924c-d904-40df-ba15-ec9696cf8992
+  modified: 2026-08-17T11:05:50.821Z
+---
+
+Address the user as "🎓Tony" (with the graduation-cap emoji prefix) when using their name in conversation, rather than plain "Tony".

.github/workflows/dev-cicd.yml

@@ -3,14 +3,99 @@ name: CI CD
 
 on:
   push:
-    branches: "*" 
+    branches: "*"
     tags: 'v*.*.*'
 
+permissions:
+  contents: write
+
 jobs:
+  get-version:
+    name: Detect version bump
+    runs-on: ubuntu-latest
+    outputs:
+      tag_name: ${{ steps.compare.outputs.tag_name }}
+      should_release: ${{ steps.compare.outputs.should_release }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v7
+        with:
+          python-version: '3.12'
+
+      - name: Install packaging
+        run: pip install packaging
+
+      - name: Compare setup.py version against existing tags
+        id: compare
+        shell: python
+        run: |
+          import os
+          import re
+          import subprocess
+          from packaging.version import Version, InvalidVersion
+
+          with open("setup.py") as f:
+              content = f.read()
+          match = re.search(r'version\s*=\s*["\']([^"\']+)["\']', content)
+          if not match:
+              raise SystemExit("Could not find version= in setup.py")
+          raw_version = match.group(1)
+          current = Version(raw_version)
+          tag_name = f"v{raw_version}"
+
+          existing_tags = subprocess.run(
+              ["git", "tag", "-l"], capture_output=True, text=True, check=True
+          ).stdout.splitlines()
+
+          latest_version = None
+          latest_tag = None
+          for t in existing_tags:
+              if not t.startswith("v"):
+                  continue
+              try:
+                  v = Version(t[1:])
+              except InvalidVersion:
+                  continue
+              if latest_version is None or v > latest_version:
+                  latest_version = v
+                  latest_tag = t
+
+          print(f"setup.py version: {raw_version} ({tag_name})")
+          print(f"latest tagged version: {latest_tag or '(none)'}")
+
+          if latest_version is not None and current < latest_version:
+              raise SystemExit(
+                  f"::error::setup.py version {raw_version} is lower than latest "
+                  f"tagged version {latest_tag}. Version must not decrease."
+              )
+
+          tag_exists = tag_name in existing_tags
+          on_main = os.environ["GITHUB_REF"] == "refs/heads/main"
+          should_release = on_main and not tag_exists
+
+          if tag_exists:
+              print(f"Tag {tag_name} already exists, skipping release.")
+          elif not on_main:
+              print(f"Version {raw_version} not yet tagged, but not on main; skipping release.")
+          else:
+              print(f"Will tag and release {tag_name}.")
+
+          gh_output = os.environ["GITHUB_OUTPUT"]
+          with open(gh_output, "a") as f:
+              f.write(f"tag_name={tag_name}\n")
+              f.write(f"should_release={'true' if should_release else 'false'}\n")
+
   test:
     # name: Test on ${{ matrix.os }} - Python ${{ matrix.python-version }}
     name: Test on ${{ matrix.os }} py3.${{ matrix.python3-version }}
     runs-on: ${{ matrix.os }}-latest
+    timeout-minutes: 20
     # continue-on-error: true  # Allow continue to build even if tests fail
     continue-on-error: ${{ matrix.python3-version != '12' }}
     strategy:
@@ -24,7 +109,7 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       # - name: Cache pip
       #   uses: actions/cache@v4
@@ -64,7 +149,7 @@ jobs:
           echo "No dependencies to install on Windows."
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
           python-version: 3.${{ matrix.python3-version }}
           cache: 'pip'
@@ -91,31 +176,33 @@ jobs:
           else
             source venv/bin/activate
           fi
-          pytest -n 4 -v --cache-clear --cov=helab --junitxml=junit.xml -o junit_family=legacy
+            pytest -n 4 --verbose --cache-clear --cov=helab --junitxml=junit.xml -o junit_family=legacy --reruns 5 --reruns-delay 2 --timeout=120 --timeout-method=thread
 
+#          pytest -n 1 -v --cache-clear --cov=helab --junitxml=junit.xml -o junit_family=legacy
 #          pytest -n 8 -v --cache-clear --cov=helab --junit-xml=pytest-report.xml
 
       - name: Upload Test Results
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: test-results-${{ matrix.os }}-py3${{ matrix.python3-version }}
           path: junit.xml
 
       - name: Upload test results to Codecov
         if: ${{ !cancelled() }}
-        uses: codecov/test-results-action@v1
+        uses: codecov/codecov-action@v7
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+          report_type: test_results
 
       - name: Run test with code coverage report
         if: matrix.python3-version == '12' && matrix.os == 'macos'
         run: |  
           source venv/bin/activate
-          pytest --cov=helab --cov-report=xml --cov-report=term --ignore=tests/test_typing.py
+          pytest --cov=helab --cov-report=xml --cov-report=term --ignore=tests/test_typing.py --cache-clear --timeout=120 --timeout-method=thread
 
       - name: Upload Code Coverage Report
         if: matrix.python3-version == '12' && matrix.os == 'macos'
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v7
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
@@ -138,7 +225,7 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       # - name: Cache pip
       #   uses: actions/cache@v4
@@ -178,7 +265,7 @@ jobs:
             libopengl0
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
           python-version: 3.${{ matrix.python3-version }}
           cache: 'pip'
@@ -208,7 +295,7 @@ jobs:
           pyinstaller HeLab.spec --clean -y
 
       - name: Archive build artifacts
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: build-${{ matrix.os }}-py3${{ matrix.python3-version }}
           # name: build-${{ matrix.os }}-py${{ format('{0}', matrix.python-version) | replace('.','') }}
@@ -223,23 +310,24 @@ jobs:
 
   release:
     name: Create Release on Tag
-    needs: [test, build]
+    needs: [get-version, test, build]
+    if: needs.get-version.outputs.should_release == 'true'
     runs-on: ubuntu-latest
     steps:
       - name: Download macOS Build Artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: build-macos-py312
           path: dist/macos
 
       - name: Download Windows Build Artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: build-windows-py312
           path: dist/windows
 
       - name: Download Ubuntu Build Artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: build-ubuntu-py312
           path: dist/ubuntu
@@ -260,9 +348,8 @@ jobs:
           zip -r -9 HeLab-ubuntu.zip HeLab
 
       - name: Prepare Release Body
-        # if: startsWith(github.ref, 'refs/tags/')
         run: |
-          RELEASE_BODY="## Release ${{ github.ref_name }}
+          RELEASE_BODY="## Release ${{ needs.get-version.outputs.tag_name }}
 
           **Date:** $(date +'%Y-%m-%d %H:%M') UTC
 
@@ -275,23 +362,23 @@ jobs:
           - **macOS ARM64** build (Python 3.12)
           - **Windows Intel64** build (Python 3.12)
           - **Ubuntu Intel64** build (Python 3.12)
-          
+
           **Note:** This is an automated release. Please verify builds before production use."
-          
+
           echo "RELEASE_BODY<<EOF" >> $GITHUB_ENV
           echo "$RELEASE_BODY" >> $GITHUB_ENV
           echo "EOF" >> $GITHUB_ENV
-          
+
           echo "Release body preview:"
           echo "$RELEASE_BODY"
 
-      - name: Create Release and Upload Assets on Tag
-        if: github.ref_type == 'tag'
+      - name: Create Release and Upload Assets on Version Bump
         uses: ncipollo/release-action@v1
         with:
-          token: ${{ secrets.PAT_TOKEN }}
-          tag: ${{ github.ref_name }}
-          name: "Automated Release ${{ github.ref_name }}"
+          token: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ needs.get-version.outputs.tag_name }}
+          commit: ${{ github.sha }}
+          name: "Automated Release ${{ needs.get-version.outputs.tag_name }}"
           body: ${{ env.RELEASE_BODY }}
           draft: true
           prerelease: true
@@ -300,18 +387,3 @@ jobs:
             dist/windows/HeLab-windows.zip
             dist/ubuntu/HeLab-ubuntu.zip
 
-      # - name: Create Release and Upload Assets on Tag 2
-      #   if: startsWith(github.ref, 'refs/tags/')
-      #   uses: ncipollo/release-action@v1
-      #   with:
-      #     token: ${{ secrets.PAT_TOKEN }}
-      #     tag: ${{ github.ref_name }}
-      #     name: "Automated Release ${{ github.ref_name }}"
-      #     body: ${{ env.RELEASE_BODY }}
-      #     draft: true
-      #     prerelease: true
-      #     artifacts: |
-      #       dist/macos/HeLab-macos.zip
-      #       dist/windows/HeLab-windows.zip
-      #       dist/ubuntu/HeLab-ubuntu.zip
-

.gitignore

@@ -72,7 +72,7 @@ CMakeLists.txt.user*
 *.dll
 *.exe
 
-.idea
+# .idea
 .qtcreator
 env
 HELIUM.pyproject*
@@ -86,3 +86,24 @@ Icon?
 helab.egg-info
 coverage.xml
 .coverage
+helab_tempfiles
+helab_caches
+helab_temps
+*.ipynb
+coverage.xml
+helab_main.prof
+*.log
+mprofile_*.dat
+profile.html
+profile.json
+.pytest_cache
+.idea/misc.xml
+.idea/modules.xml
+.coverage.*
+.coverage*
+junit.xml
+_server alias/
+.ai/temp/
+venv
+side_projects/rga_visualiser/RGAData
+venv.nosync

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "legacy/tdc_autoconverter"]
+	path = legacy/tdc_autoconverter
+	url = https://github.com/HeBECANU/tdc_autoconverter
+	branch = master