Removed AI project files and demo subprojects

.github/workflows/npm-grunt.yml

@@ -0,0 +1,28 @@
+name: NodeJS with Grunt
+
+on:
+  push:
+    branches: [ "develop" ]
+  pull_request:
+    branches: [ "develop" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [18.x, 20.x, 22.x]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v4
+      with:
+        node-version: ${{ matrix.node-version }}
+
+    - name: Build
+      run: |
+        npm install
+        grunt

.github/workflows/npm-publish.yml

@@ -0,0 +1,33 @@
+# This workflow will run tests using node and then publish a package to GitHub Packages when a release is created
+# For more information see: https://docs.github.com/en/actions/publishing-packages/publishing-nodejs-packages
+
+name: Node.js Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+      - run: npm ci
+      - run: npm test
+
+  publish-npm:
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          registry-url: https://registry.npmjs.org/
+      - run: npm ci
+      - run: npm publish
+        env:
+          NODE_AUTH_TOKEN: ${{secrets.npm_token}}

sbol_utilities/conversion.py

@@ -114,12 +114,25 @@ def convert2to3(sbol2_doc: Union[str, sbol2.Document], namespaces=None, use_nati
     # TODO: remove workaround after conversion errors fixed in https://github.com/sboltools/sbolgraph/issues/14
     # add in the missing namespace fields where possible, defaulting otherwise
     # TODO: add check for non-TopLevel? See https://github.com/SynBioDex/pySBOL3/issues/295
-    needs_namespace = {o for o in doc.objects if o.namespace is None}
-    for n in namespaces:
-        assignable = {o for o in needs_namespace if o.identity.startswith(n)}
-        for a in assignable:
-            a.namespace = n
-        needs_namespace = needs_namespace - assignable
+    # Namespace Assignment
+needs_namespace = {o for o in doc.objects if o.namespace is None}
+for n in namespaces:
+    assignable = {o for o in needs_namespace if o.identity.startswith(n)}
+    for a in assignable:
+        a.namespace = n
+    needs_namespace = needs_namespace - assignable
+for o in needs_namespace:
+    p = urllib.parse.urlparse(o.identity)
+    server = urllib.parse.urlunparse([p.scheme, p.netloc, '', '', '', ''])
+    o.namespace = server
+
+# Sequence Inference
+for s in (o for o in doc.objects if isinstance(o, sbol3.Component)):
+    if len(s.sequences) != 1:
+        continue
+    for f in (f for f in s.features if isinstance(f, sbol3.SequenceFeature) or isinstance(f, sbol3.SubComponent)):
+        for loc in f.locations:
+            loc.sequence = s.sequences[0]
     for o in needs_namespace:  # if no supplied namespace matches, default to scheme//netloc
         # figure out the server to access from the URL
         p = urllib.parse.urlparse(o.identity)