Merge pull request #124 from argonne-lcf/dev

- Update ChemGraph container and add Kubernetes deployment. Add Kubernetes deployment support #123
- Add execution layer to ChemGraph, including EnsembleLauncher, Parsl, Globus compute and Globus transfer. Add - pluggable execution backends and backend-agnostic HPC MCP servers #120 Modified the EL backend implemenations, and added a EL backend test #127
- Add initial Academy integration Add pluggable execution backends and backend-agnostic HPC MCP servers #120
- Updates package metadata to version 0.5.0 and fixes source-checkout version reporting so UI deployments do not show unknown.
- Modernizes the Streamlit UI with modular pages, improved chat/session behavior, available-calculator display, better math/report rendering, HTML report downloads, and build/host metadata.
- Adds calculator availability detection during agent initialization and improves calculator selection, including xTB/TBLite alias handling.
- Expands agent workflows with human-in-the-loop support, single-agent routing tests, retry/session fixes, and safer state serialization.
- Adds and improves CLI, memory/session persistence, model routing, MCP client support, RAG, XANES, and evaluation tooling.
- Adds Kubernetes, GHCR, Streamlit Cloud, HPC, and MCP deployment documentation and examples.
Improves CI reliability with dependency pins, Windows serializer fixes, Ruff cleanup, and expanded tests.

Author: keceli

.github/workflows/dependency_tests.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.10", "3.11", "3.12", "3.13"]
-        install_extras: [core, calculators, uma, ui, parsl, viz]
+        install_extras: [core, calculators, uma, ui, parsl, xanes, rag]
 
     steps:
     - uses: actions/checkout@v4
@@ -74,9 +74,19 @@ jobs:
             'uma': ['fairchem.core', 'e3nn'],
             'ui': ['streamlit', 'stmol'],
             'parsl': ['parsl'],
-            'viz': ['pyppeteer', 'grandalf', 'nest_asyncio']
+            'xanes': ['parsl'],
+            'rag': [
+                'faiss',
+                'langchain_text_splitters',
+                'langchain_huggingface',
+                'sentence_transformers',
+                'fitz',
+            ],
         }
 
+        if extras == 'xanes' and sys.version_info >= (3, 11):
+            extra_packages['xanes'].append('mp_api')
+
         if extras != 'core':
              # Check packages for specific extra
              if extras in extra_packages:

.github/workflows/ghcr-publish.yml

@@ -4,6 +4,9 @@ on:
   push:
     tags:
       - "v*"
+    branches:
+      - feature_k8s
+      - dev
   workflow_dispatch:
 
 permissions:
@@ -20,9 +23,6 @@ jobs:
           - arch: amd64
             platform: linux/amd64
             dockerfile: Dockerfile
-          - arch: arm64
-            platform: linux/arm64
-            dockerfile: Dockerfile.arm
 
     steps:
       - name: Checkout code
@@ -84,10 +84,11 @@ jobs:
           images: ${{ steps.prep.outputs.image }}
           tags: |
             type=ref,event=tag
+            type=ref,event=branch
             type=sha,prefix=sha-
-            type=raw,value=latest
+            type=raw,value=latest,enable=${{ startsWith(github.ref, 'refs/tags/') }}
 
-      - name: Create and push multi-arch manifests
+      - name: Create and push manifests
         env:
           IMAGE: ${{ steps.prep.outputs.image }}
           TAGS: ${{ steps.meta.outputs.tags }}
@@ -96,11 +97,10 @@ jobs:
             [ -z "$tag" ] && continue
             docker buildx imagetools create \
               -t "$tag" \
-              "${IMAGE}:build-${GITHUB_SHA}-amd64" \
-              "${IMAGE}:build-${GITHUB_SHA}-arm64"
+              "${IMAGE}:build-${GITHUB_SHA}-amd64"
           done <<< "$TAGS"
 
-      - name: Inspect latest manifest
+      - name: Inspect manifest
         env:
           IMAGE: ${{ steps.prep.outputs.image }}
-        run: docker buildx imagetools inspect "${IMAGE}:latest"
+        run: docker buildx imagetools inspect "${IMAGE}:${GITHUB_REF_NAME}"

.github/workflows/test-pypi-package.yml

@@ -34,8 +34,7 @@ jobs:
       run: |
         python -c "import chemgraph; print('ChemGraph imported successfully')"
         python -c "from chemgraph.cli import main; print('CLI module imported successfully')"
-        # Test that CLI command is available
-        chemgraph --help || echo "CLI help command executed"
+        chemgraph --help
 
     - name: Run basic import tests
       run: |

.gitignore

@@ -57,5 +57,8 @@ test.csv
 nwchem/
 nwchem.nwi
 nwchem.nwo
-
+config.toml
 vib*.traj
+
+# Kubernetes secrets (keep secrets.yaml.template, ignore actual secrets)
+k8s/secrets.yaml