Merge remote-tracking branch 'origin/main' into feature/image-search-new

.github/workflows/test.yaml

@@ -81,6 +81,7 @@ jobs:
       - name: Run Playwright tests
         run: |
           cd lynxkite-app/web
+          npm run build
           npm run test
 
       - uses: actions/upload-artifact@v4

Dockerfile

@@ -5,12 +5,16 @@ USER node
 ENV HOME=/home/node PATH=/home/node/.local/bin:$PATH
 WORKDIR $HOME/app
 COPY --chown=node . $HOME/app
-RUN uv venv && uv pip install \
+ENV GIT_SSH_COMMAND="ssh -i /run/secrets/LYNXSCRIBE_DEPLOY_KEY -o StrictHostKeyChecking=no"
+RUN --mount=type=secret,id=LYNXSCRIBE_DEPLOY_KEY,mode=0444,required=true \
+  uv venv && uv pip install \
   -e lynxkite-core \
   -e lynxkite-app \
   -e lynxkite-graph-analytics \
   -e lynxkite-bio \
-  -e lynxkite-pillow-example
+  -e lynxkite-lynxscribe \
+  -e lynxkite-pillow-example \
+  chromadb openai
 WORKDIR $HOME/app/examples
 ENV PORT=7860
 CMD ["uv", "run", "lynxkite"]

biome.json

@@ -1,6 +1,10 @@
 {
+  "files": {
+    "ignore": ["**/*.lynxkite.json"]
+  },
   "formatter": {
     "ignore": ["**/node_modules/**", "**/dist/**"],
+    "lineWidth": 100,
     "indentStyle": "space"
   },
   "linter": {
@@ -20,6 +24,7 @@
         "useKeyWithClickEvents": "off",
         "useValidAnchor": "off",
         "useButtonType": "off",
+        "noAutofocus": "off",
         "noNoninteractiveTabindex": "off"
       }
     }

examples/{LynxScribe RAG Chatbot.lynxkite.json → Generative drug screening.lynxkite.json}

@@ -1,77 +1,56 @@
 {
   "edges": [
     {
-      "id": "xy-edge__Truncate history 1output-Chat processor 1processor",
-      "source": "Truncate history 1",
+      "id": "Import file 2 Query GenMol 1",
+      "source": "Import file 2",
       "sourceHandle": "output",
-      "target": "Chat processor 1",
-      "targetHandle": "processor"
+      "target": "Query GenMol 1",
+      "targetHandle": "bundle"
     },
     {
-      "id": "xy-edge__Mask 1output-Chat processor 1processor",
-      "source": "Mask 1",
+      "id": "Import file 1 MSA-search 1",
+      "source": "Import file 1",
       "sourceHandle": "output",
-      "target": "Chat processor 1",
-      "targetHandle": "processor"
+      "target": "MSA-search 1",
+      "targetHandle": "bundle"
     },
     {
-      "id": "xy-edge__Mask 2output-Chat processor 1processor",
-      "source": "Mask 2",
+      "id": "Query GenMol 1 Query DiffDock 1",
+      "source": "Query GenMol 1",
       "sourceHandle": "output",
-      "target": "Chat processor 1",
-      "targetHandle": "processor"
+      "target": "Query DiffDock 1",
+      "targetHandle": "ligands"
     },
     {
-      "id": "xy-edge__Input chat 1output-Test Chat API 2message",
-      "source": "Input chat 1",
+      "id": "Query DiffDock 1 View molecules 1",
+      "source": "Query DiffDock 1",
       "sourceHandle": "output",
-      "target": "Test Chat API 2",
-      "targetHandle": "message"
+      "target": "View molecules 1",
+      "targetHandle": "bundle"
     },
     {
-      "id": "xy-edge__Test Chat API 2output-View 1input",
-      "source": "Test Chat API 2",
+      "id": "MSA-search 1 Query OpenFold2 1",
+      "source": "MSA-search 1",
       "sourceHandle": "output",
-      "target": "View 1",
-      "targetHandle": "input"
+      "target": "Query OpenFold2 1",
+      "targetHandle": "bundle"
     },
     {
-      "id": "LynxScribe RAG Graph Chatbot Backend 1 Test Chat API 2",
-      "source": "LynxScribe RAG Graph Chatbot Backend 1",
+      "id": "Query OpenFold2 1 View molecules 3",
+      "source": "Query OpenFold2 1",
       "sourceHandle": "output",
-      "target": "Test Chat API 2",
-      "targetHandle": "chat_api"
+      "target": "View molecules 3",
+      "targetHandle": "bundle"
     },
     {
-      "id": "Chat processor 1 LynxScribe RAG Graph Chatbot Backend 1",
-      "source": "Chat processor 1",
+      "id": "Query OpenFold2 1 Query DiffDock 1",
+      "source": "Query OpenFold2 1",
       "sourceHandle": "output",
-      "target": "LynxScribe RAG Graph Chatbot Backend 1",
-      "targetHandle": "chat_processor"
-    },
-    {
-      "id": "Cloud-sourced File Listing 1 LynxScribe Text RAG Loader 1",
-      "source": "Cloud-sourced File Listing 1",
-      "sourceHandle": "output",
-      "target": "LynxScribe Text RAG Loader 1",
-      "targetHandle": "file_urls"
-    },
-    {
-      "id": "LynxScribe Text RAG Loader 1 LynxScribe RAG Graph Chatbot Builder 1",
-      "source": "LynxScribe Text RAG Loader 1",
-      "sourceHandle": "output",
-      "target": "LynxScribe RAG Graph Chatbot Builder 1",
-      "targetHandle": "rag_graph"
-    },
-    {
-      "id": "LynxScribe RAG Graph Chatbot Builder 1 LynxScribe RAG Graph Chatbot Backend 1",
-      "source": "LynxScribe RAG Graph Chatbot Builder 1",
-      "sourceHandle": "output",
-      "target": "LynxScribe RAG Graph Chatbot Backend 1",
-      "targetHandle": "knowledge_base"
+      "target": "Query DiffDock 1",
+      "targetHandle": "proteins"
     }
   ],
-  "env": "LynxScribe",
+  "env": "LynxKite Graph Analytics",
   "nodes": [
     {
       "data": {
@@ -81,7 +60,7 @@
         "error": null,
         "meta": {
           "inputs": {},
-          "name": "Input chat",
+          "name": "Import file",
           "outputs": {
             "output": {
               "name": "output",
@@ -92,9 +71,62 @@
             }
           },
           "params": {
-            "chat": {
+            "file_format": {
+              "default": "csv",
+              "groups": {
+                "csv": [
+                  {
+                    "default": "<from file>",
+                    "name": "columns",
+                    "type": {
+                      "type": "<class 'str'>"
+                    }
+                  },
+                  {
+                    "default": "<auto>",
+                    "name": "separator",
+                    "type": {
+                      "type": "<class 'str'>"
+                    }
+                  }
+                ],
+                "excel": [
+                  {
+                    "default": "Sheet1",
+                    "name": "sheet_name",
+                    "type": {
+                      "type": "<class 'str'>"
+                    }
+                  }
+                ],
+                "json": [],
+                "parquet": []
+              },
+              "name": "file_format",
+              "selector": {
+                "default": "csv",
+                "name": "file_format",
+                "type": {
+                  "enum": [
+                    "csv",
+                    "parquet",
+                    "json",
+                    "excel"
+                  ]
+                }
+              },
+              "type": "group"
+            },
+            "file_path": {
+              "default": null,
+              "name": "file_path",
+              "type": {
+                "type": "<class 'str'>"
+              }
+            },
+            "table_name": {
               "default": null,
-              "name": "chat",
+              "name": "table_name",
               "type": {
                 "type": "<class 'str'>"
               }
@@ -103,635 +135,636 @@
           "type": "basic"
         },
         "params": {
-          "chat": "Wgo is Gabor?"
+          "columns": "<from file>",
+          "file_format": "csv",
+          "file_path": "uploads/protein.csv",
+          "separator": "<auto>",
+          "table_name": ""
         },
         "status": "done",
-        "title": "Input chat"
+        "title": "Import file"
       },
       "dragHandle": ".bg-primary",
-      "height": 186.0,
-      "id": "Input chat 1",
-      "parentId": null,
+      "height": 487.0,
+      "id": "Import file 1",
       "position": {
-        "x": -2606.8829929570456,
-        "y": -648.2654341415332
+        "x": -755.0582906538923,
+        "y": 543.770372030674
       },
       "type": "basic",
-      "width": 259.0
-    },
-    {
-      "data": {
-        "display": {
-          "dataframes": {
-            "df": {
-              "columns": ["answer"],
-              "data": [
-                [
-                  "Lynx Analytics has two notable professionals named G\u00e1bor. Could you please specify which G\u00e1bor you are inquiring about?\n\n- **G\u00e1bor Benedek**: Chief Innovation Officer & Co-founder at Lynx Analytics. He specializes in economic and business simulations, social network analysis, data mining, and predictive analytics. He has an academic background as a former Associate Professor at Corvinus University of Budapest and has founded several data-related companies.\n\n- **G\u00e1bor Kriv\u00e1chy**: Country Manager at Lynx Analytics in Hungary. He is an experienced technology executive with a background in system implementation, integration, and project management, particularly in SAP implementations.\n\nLet me know which G\u00e1bor's details you would like to learn more about!"
-                ]
-              ]
-            }
-          }
-        },
-        "error": null,
-        "meta": {
-          "inputs": {
-            "input": {
-              "name": "input",
-              "position": "left",
-              "type": {
-                "type": "<class 'inspect._empty'>"
-              }
-            }
-          },
-          "name": "View",
-          "outputs": {},
-          "params": {},
-          "type": "table_view"
-        },
-        "params": {},
-        "status": "done",
-        "title": "View"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 950.0,
-      "id": "View 1",
-      "parentId": null,
-      "position": {
-        "x": -754.9225960536905,
-        "y": -643.161064357758
-      },
-      "type": "table_view",
-      "width": 1256.0
+      "width": 439.0
     },
     {
       "data": {
+        "__execution_delay": 0.0,
+        "collapsed": null,
         "display": null,
         "error": null,
         "meta": {
           "inputs": {},
-          "name": "Truncate history",
+          "name": "Import file",
           "outputs": {
             "output": {
               "name": "output",
-              "position": "top",
+              "position": "right",
               "type": {
                 "type": "None"
               }
             }
           },
           "params": {
-            "max_tokens": {
-              "default": 10000.0,
-              "name": "max_tokens",
+            "file_format": {
+              "default": "csv",
+              "groups": {
+                "csv": [
+                  {
+                    "default": "<from file>",
+                    "name": "columns",
+                    "type": {
+                      "type": "<class 'str'>"
+                    }
+                  },
+                  {
+                    "default": "<auto>",
+                    "name": "separator",
+                    "type": {
+                      "type": "<class 'str'>"
+                    }
+                  }
+                ],
+                "excel": [
+                  {
+                    "default": "Sheet1",
+                    "name": "sheet_name",
+                    "type": {
+                      "type": "<class 'str'>"
+                    }
+                  }
+                ],
+                "json": [],
+                "parquet": []
+              },
+              "name": "file_format",
+              "selector": {
+                "default": "csv",
+                "name": "file_format",
+                "type": {
+                  "enum": [
+                    "csv",
+                    "parquet",
+                    "json",
+                    "excel"
+                  ]
+                }
+              },
+              "type": "group"
+            },
+            "file_path": {
+              "default": null,
+              "name": "file_path",
               "type": {
-                "type": "<class 'int'>"
+                "type": "<class 'str'>"
+              }
+            },
+            "table_name": {
+              "default": null,
+              "name": "table_name",
+              "type": {
+                "type": "<class 'str'>"
               }
             }
           },
           "type": "basic"
         },
         "params": {
-          "max_tokens": 10000.0
+          "columns": "<from file>",
+          "file_format": "csv",
+          "file_path": "uploads/molecules.csv",
+          "separator": "<auto>",
+          "table_name": null
         },
         "status": "done",
-        "title": "Truncate history"
+        "title": "Import file"
       },
       "dragHandle": ".bg-primary",
-      "height": 200.0,
-      "id": "Truncate history 1",
-      "parentId": null,
+      "height": 436.0,
+      "id": "Import file 2",
       "position": {
-        "x": -1536.508533731351,
-        "y": 728.1204075546109
+        "x": 62.887657256500006,
+        "y": 1380.6697994924546
       },
       "type": "basic",
-      "width": 200.0
+      "width": 311.0
     },
     {
       "data": {
-        "__execution_delay": null,
-        "collapsed": false,
         "display": null,
         "error": null,
         "meta": {
           "inputs": {
-            "processor": {
-              "name": "processor",
-              "position": "bottom",
-              "type": {
-                "type": "<class 'inspect._empty'>"
-              }
-            }
-          },
-          "name": "Chat processor",
-          "outputs": {
-            "output": {
-              "name": "output",
-              "position": "top",
+            "bundle": {
+              "name": "bundle",
+              "position": "left",
               "type": {
-                "type": "None"
+                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
               }
             }
           },
-          "params": {},
-          "type": "basic"
-        },
-        "params": {},
-        "status": "done",
-        "title": "Chat processor"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 89.0,
-      "id": "Chat processor 1",
-      "parentId": null,
-      "position": {
-        "x": -1527.1027075359414,
-        "y": 605.2129408898476
-      },
-      "type": "basic",
-      "width": 416.0
-    },
-    {
-      "data": {
-        "__execution_delay": 0.0,
-        "collapsed": null,
-        "display": null,
-        "error": null,
-        "meta": {
-          "inputs": {},
-          "name": "Mask",
+          "name": "Query GenMol",
           "outputs": {
             "output": {
               "name": "output",
-              "position": "top",
+              "position": "right",
               "type": {
                 "type": "None"
               }
             }
           },
           "params": {
-            "exceptions": {
-              "default": "",
-              "name": "exceptions",
+            "molecule_column": {
+              "default": null,
+              "name": "molecule_column",
               "type": {
                 "type": "<class 'str'>"
               }
             },
-            "mask_pattern": {
-              "default": "",
-              "name": "mask_pattern",
+            "molecule_table": {
+              "default": null,
+              "name": "molecule_table",
               "type": {
                 "type": "<class 'str'>"
               }
             },
-            "name": {
-              "default": "",
-              "name": "name",
+            "noise": {
+              "default": 0.2,
+              "name": "noise",
               "type": {
-                "type": "<class 'str'>"
+                "type": "<class 'float'>"
               }
             },
-            "regex": {
-              "default": "",
-              "name": "regex",
+            "num_molecules": {
+              "default": 5.0,
+              "name": "num_molecules",
+              "type": {
+                "type": "<class 'int'>"
+              }
+            },
+            "scoring": {
+              "default": "QED",
+              "name": "scoring",
               "type": {
                 "type": "<class 'str'>"
               }
+            },
+            "step_size": {
+              "default": 4.0,
+              "name": "step_size",
+              "type": {
+                "type": "<class 'int'>"
+              }
+            },
+            "temperature": {
+              "default": 1.0,
+              "name": "temperature",
+              "type": {
+                "type": "<class 'float'>"
+              }
             }
           },
+          "position": {
+            "x": 594.0,
+            "y": 633.0
+          },
           "type": "basic"
         },
         "params": {
-          "exceptions": "[email protected],[email protected],[email protected],[email protected]",
-          "mask_pattern": "masked_email_address_{}",
-          "name": "email",
-          "regex": "([a-z0-9!#$%&'*+\\/=?^_`{|.}~-]+@(?:[a-z0-9](?:[a-z0-9-]*[a-z0-9])?\\.)+[a-z0-9](?:[a-z0-9-]*[a-z0-9])?)"
+          "molecule_column": null,
+          "molecule_table": null,
+          "noise": 0.2,
+          "num_molecules": 5.0,
+          "scoring": "QED",
+          "step_size": 4.0,
+          "temperature": 1.0
         },
         "status": "done",
-        "title": "Mask"
+        "title": "Query GenMol"
       },
       "dragHandle": ".bg-primary",
-      "height": 358.0,
-      "id": "Mask 1",
-      "parentId": null,
+      "height": 601.0,
+      "id": "Query GenMol 1",
       "position": {
-        "x": -1309.5065330408577,
-        "y": 731.6791509394458
+        "x": 663.3333333333335,
+        "y": 1283.3333333333335
       },
       "type": "basic",
-      "width": 313.0
+      "width": 358.0
     },
     {
       "data": {
-        "__execution_delay": 0.0,
         "collapsed": null,
         "display": null,
         "error": null,
         "meta": {
-          "inputs": {},
-          "name": "Mask",
+          "inputs": {
+            "bundle": {
+              "name": "bundle",
+              "position": "left",
+              "type": {
+                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
+              }
+            }
+          },
+          "name": "MSA-search",
           "outputs": {
             "output": {
               "name": "output",
-              "position": "top",
+              "position": "right",
               "type": {
                 "type": "None"
               }
             }
           },
           "params": {
-            "exceptions": {
-              "default": "",
-              "name": "exceptions",
+            "databases": {
+              "default": "[\"Uniref30_2302\", \"colabfold_envdb_202108\", \"PDB70_220313\"]",
+              "name": "databases",
               "type": {
                 "type": "<class 'str'>"
               }
             },
-            "mask_pattern": {
-              "default": "",
-              "name": "mask_pattern",
+            "e_value": {
+              "default": 0.0001,
+              "name": "e_value",
               "type": {
-                "type": "<class 'str'>"
+                "type": "<class 'float'>"
               }
             },
-            "name": {
-              "default": "",
-              "name": "name",
+            "iterations": {
+              "default": 1.0,
+              "name": "iterations",
               "type": {
-                "type": "<class 'str'>"
+                "type": "<class 'int'>"
               }
             },
-            "regex": {
-              "default": "",
-              "name": "regex",
+            "output_alignment_formats": {
+              "default": [
+                "fasta",
+                "a3m"
+              ],
+              "name": "output_alignment_formats",
               "type": {
-                "type": "<class 'str'>"
+                "type": "list[lynxkite_bio.nims.AlignmentFormats]"
               }
-            }
-          },
-          "type": "basic"
-        },
-        "params": {
-          "exceptions": "",
-          "mask_pattern": "masked_credit_card_number_{}",
-          "name": "credit_card",
-          "regex": "((?:(?:\\\\d{4}[- ]?){3}\\\\d{4}|\\\\d{15,16}))(?![\\\\d])"
-        },
-        "status": "done",
-        "title": "Mask"
-      },
-      "dragHandle": ".bg-primary",
-      "height": 358.0,
-      "id": "Mask 2",
-      "parentId": null,
-      "position": {
-        "x": -983.2612912523697,
-        "y": 731.5859900002104
-      },
-      "type": "basic",
-      "width": 315.0
-    },
-    {
-      "data": {
-        "__execution_delay": 0.0,
-        "collapsed": false,
-        "display": null,
-        "error": null,
-        "meta": {
-          "inputs": {
-            "chat_api": {
-              "name": "chat_api",
-              "position": "bottom",
+            },
+            "protein_column": {
+              "default": null,
+              "name": "protein_column",
               "type": {
-                "type": "<class 'inspect._empty'>"
+                "type": "<class 'str'>"
               }
             },
-            "message": {
-              "name": "message",
-              "position": "left",
+            "protein_table": {
+              "default": null,
+              "name": "protein_table",
               "type": {
-                "type": "<class 'inspect._empty'>"
+                "type": "<class 'str'>"
               }
-            }
-          },
-          "name": "Test Chat API",
-          "outputs": {
-            "output": {
-              "name": "output",
-              "position": "right",
+            },
+            "search_type": {
+              "default": "ALPHAFOLD2",
+              "name": "search_type",
               "type": {
-                "type": "None"
+                "enum": [
+                  "ALPHAFOLD2",
+                  "ESM2"
+                ]
               }
             }
           },
-          "params": {
-            "show_details": {
-              "default": false,
-              "name": "show_details",
-              "type": {
-                "type": "<class 'bool'>"
-              }
-            }
+          "position": {
+            "x": 576.0,
+            "y": 228.0
           },
           "type": "basic"
         },
-        "params": {},
+        "params": {
+          "databases": "[\"Uniref30_2302\", \"colabfold_envdb_202108\", \"PDB70_220313\"]",
+          "e_value": 0.0001,
+          "iterations": 1.0,
+          "output_alignment_formats": [
+            "fasta",
+            "a3m"
+          ],
+          "protein_column": null,
+          "protein_table": null,
+          "search_type": "ALPHAFOLD2"
+        },
         "status": "done",
-        "title": "Test Chat API"
+        "title": "MSA-search"
       },
       "dragHandle": ".bg-primary",
-      "height": 201.0,
-      "id": "Test Chat API 2",
-      "parentId": null,
+      "height": 550.0,
+      "id": "MSA-search 1",
       "position": {
-        "x": -2024.044443214723,
-        "y": -654.8412606520155
+        "x": -45.0,
+        "y": 570.0
       },
       "type": "basic",
-      "width": 906.0
+      "width": 531.0
     },
     {
       "data": {
-        "__execution_delay": 0.0,
-        "collapsed": null,
         "display": null,
         "error": null,
         "meta": {
           "inputs": {
-            "chat_processor": {
-              "name": "chat_processor",
-              "position": "bottom",
+            "ligands": {
+              "name": "ligands",
+              "position": "left",
               "type": {
-                "type": "<class 'inspect._empty'>"
+                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
               }
             },
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               "name": "output",
-              "position": "top",
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                 "type": "None"
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         "meta": {
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-              "name": "output",
-              "position": "right",
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               "type": {
-                "type": "None"
+                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
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             }
           },
+          "name": "View molecules",
+          "outputs": {},
           "params": {
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-              "default": ".jpg, .jpeg, .png",
-              "name": "accepted_file_types",
+            "color": {
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             },
-            "folder_URL": {
-              "default": "https://storage.googleapis.com/lynxkite_public_data/lynxscribe-images/image-rag-test",
-              "name": "folder_URL",
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               "type": {
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         "params": {
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-          "cloud_provider": "GCP",
-          "folder_URL": "https://storage.googleapis.com/lynxkite_public_data/lynxscribe-knowledge-graphs/lynx-chatbot"
+          "color": "spectrum",
+          "molecule_column": null,
+          "molecule_table": null
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         "status": "done",
-        "title": "Cloud-sourced File Listing"
+        "title": "View molecules"
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@@ -739,62 +772,102 @@
         "error": null,
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           "inputs": {
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-              "name": "rag_graph",
+            "bundle": {
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               "position": "left",
               "type": {
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+                "type": "<class 'lynxkite_graph_analytics.core.Bundle'>"
               }
             }
           },
-          "name": "LynxScribe RAG Graph Chatbot Builder",
+          "name": "Query OpenFold2",
           "outputs": {
             "output": {
               "name": "output",
-              "position": "top",
+              "position": "right",
               "type": {
                 "type": "None"
               }
             }
           },
           "params": {
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-              "name": "node_types",
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+              "name": "databases",
               "type": {
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-              "name": "scenario_file",
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 }

examples/{Graph RAG → Graph RAG.lynxkite.json}

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@@ -541,13 +540,6 @@
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-              "name": "model"
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examples/Model definition.lynxkite.json

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+      "source": "MSE loss 2",
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+      "target": "Concatenate 1",
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+    },
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+      "sourceHandle": "x",
+      "target": "Concatenate 1",
+      "targetHandle": "b"
+    },
+    {
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+      "source": "Input: label 1",
+      "sourceHandle": "y",
+      "target": "MSE loss 1",
+      "targetHandle": "y"
+    },
+    {
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+      "source": "MSE loss 1",
+      "sourceHandle": "loss",
+      "target": "Optimizer 1",
+      "targetHandle": "loss"
+    },
+    {
+      "id": "Concatenate 1 Neural ODE 2",
+      "source": "Concatenate 1",
+      "sourceHandle": "x",
+      "target": "Neural ODE 2",
+      "targetHandle": "x"
+    },
+    {
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+      "source": "Neural ODE 2",
+      "sourceHandle": "x",
+      "target": "MSE loss 1",
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+    }
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+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
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+              "type": {
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+              }
+            }
+          },
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+      },
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+      "id": "Input: embedding 1",
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+        "meta": {
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+              "position": "bottom",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "name": "Activation",
+          "outputs": {
+            "x": {
+              "name": "x",
+              "position": "top",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "params": {
+            "type": {
+              "default": "1",
+              "name": "type",
+              "type": {
+                "enum": [
+                  "ReLU",
+                  "LeakyReLU",
+                  "Tanh",
+                  "Mish"
+                ]
+              }
+            }
+          },
+          "type": "basic"
+        },
+        "params": {
+          "type": 1.0
+        },
+        "status": "planned",
+        "title": "Activation"
+      },
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+      "id": "Activation 1",
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+        "meta": {
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+            "x": {
+              "name": "x",
+              "position": "bottom",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "name": "LSTM",
+          "outputs": {
+            "h": {
+              "name": "h",
+              "position": "top",
+              "type": {
+                "type": "tensor"
+              }
+            },
+            "x": {
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+                "type": "tensor"
+              }
+            }
+          },
+          "params": {},
+          "type": "basic"
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+        "params": {},
+        "status": "planned",
+        "title": "LSTM"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "LSTM 1",
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+                "type": "tensor"
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+          "name": "Input: zeros",
+          "outputs": {
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+              "name": "x",
+              "position": "top",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "params": {},
+          "type": "basic"
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+        "status": "planned",
+        "title": "Input: zeros"
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+      "height": 200.0,
+      "id": "Input: zeros 1",
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+        "meta": {
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+              "name": "input",
+              "position": "top",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "name": "Recurrent chain",
+          "outputs": {
+            "output": {
+              "name": "output",
+              "position": "bottom",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "params": {},
+          "type": "basic"
+        },
+        "params": {},
+        "status": "planned",
+        "title": "Recurrent chain"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "Recurrent chain 1",
+      "position": {
+        "x": 1224.6603040746108,
+        "y": 135.44839862151363
+      },
+      "type": "basic",
+      "width": 200.0
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+    {
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+        "display": null,
+        "error": null,
+        "meta": {
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+              "name": "x",
+              "position": "bottom",
+              "type": {
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+              }
+            },
+            "y": {
+              "name": "y",
+              "position": "bottom",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "name": "MSE loss",
+          "outputs": {
+            "loss": {
+              "name": "loss",
+              "position": "top",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "params": {},
+          "type": "basic"
+        },
+        "params": {},
+        "status": "planned",
+        "title": "MSE loss"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "MSE loss 1",
+      "position": {
+        "x": 915.0,
+        "y": -900.0
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+      "type": "basic",
+      "width": 200.0
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+    {
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+        "collapsed": true,
+        "display": null,
+        "error": null,
+        "meta": {
+          "inputs": {},
+          "name": "Input: label",
+          "outputs": {
+            "y": {
+              "name": "y",
+              "position": "top",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "params": {},
+          "type": "basic"
+        },
+        "params": {},
+        "status": "planned",
+        "title": "Input: label"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "Input: label 1",
+      "position": {
+        "x": 1095.0,
+        "y": -450.0
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+      "type": "basic",
+      "width": 200.0
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+        "meta": {
+          "inputs": {
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+              "name": "loss",
+              "position": "bottom",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "name": "Optimizer",
+          "outputs": {},
+          "params": {
+            "lr": {
+              "default": 0.001,
+              "name": "lr",
+              "type": {
+                "type": "<class 'float'>"
+              }
+            },
+            "type": {
+              "default": "1",
+              "name": "type",
+              "type": {
+                "enum": [
+                  "AdamW",
+                  "Adafactor",
+                  "Adagrad",
+                  "SGD",
+                  "Lion",
+                  "Paged AdamW",
+                  "Galore AdamW"
+                ]
+              }
+            }
+          },
+          "type": "basic"
+        },
+        "params": {
+          "lr": 0.001,
+          "type": 1.0
+        },
+        "status": "planned",
+        "title": "Optimizer"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 247.0,
+      "id": "Optimizer 1",
+      "position": {
+        "x": 915.3430278730226,
+        "y": -1268.0577550022126
+      },
+      "type": "basic",
+      "width": 190.0
+    },
+    {
+      "data": {
+        "display": null,
+        "error": null,
+        "meta": {
+          "inputs": {
+            "x": {
+              "name": "x",
+              "position": "bottom",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "name": "Neural ODE",
+          "outputs": {
+            "x": {
+              "name": "x",
+              "position": "top",
+              "type": {
+                "type": "tensor"
+              }
+            }
+          },
+          "params": {
+            "absolute_tolerance": {
+              "default": null,
+              "name": "absolute_tolerance",
+              "type": {
+                "type": "None"
+              }
+            },
+            "method": {
+              "default": "1",
+              "name": "method",
+              "type": {
+                "enum": [
+                  "dopri8",
+                  "dopri5",
+                  "bosh3",
+                  "fehlberg2",
+                  "adaptive_heun",
+                  "euler",
+                  "midpoint",
+                  "rk4",
+                  "explicit_adams",
+                  "implicit_adams"
+                ]
+              }
+            },
+            "relative_tolerance": {
+              "default": null,
+              "name": "relative_tolerance",
+              "type": {
+                "type": "None"
+              }
+            }
+          },
+          "type": "basic"
+        },
+        "params": {
+          "absolute_tolerance": null,
+          "method": 1.0,
+          "relative_tolerance": null
+        },
+        "status": "planned",
+        "title": "Neural ODE"
+      },
+      "dragHandle": ".bg-primary",
+      "height": 200.0,
+      "id": "Neural ODE 2",
+      "position": {
+        "x": 342.3226409443945,
+        "y": -687.1882072175634
+      },
+      "type": "basic",
+      "width": 200.0
+    }
+  ]
+}

examples/fake_data.py

@@ -0,0 +1,16 @@
+from lynxkite.core.ops import op
+from faker import Faker
+import pandas as pd
+
+faker = Faker()
+
+
+@op("LynxKite Graph Analytics", "Fake data")
+def fake(*, n=10):
+    df = pd.DataFrame(
+        {
+            "name": [faker.name() for _ in range(n)],
+            "address": [faker.address() for _ in range(n)],
+        }
+    )
+    return df

examples/requirements.txt

@@ -0,0 +1 @@
+Faker

examples/word2vec.py

@@ -0,0 +1,26 @@
+from lynxkite.core.ops import op
+import staticvectors
+import pandas as pd
+
+ENV = "LynxKite Graph Analytics"
+
+
+@op(ENV, "Word2vec for the top 1000 words", slow=True)
+def word2vec_1000():
+    model = staticvectors.StaticVectors("neuml/word2vec-quantized")
+    df = pd.read_csv(
+        "https://gist.githubusercontent.com/deekayen/4148741/raw/98d35708fa344717d8eee15d11987de6c8e26d7d/1-1000.txt",
+        names=["word"],
+    )
+    df["embedding"] = model.embeddings(df.word.tolist()).tolist()
+    return df
+
+
+@op(ENV, "Take first N")
+def first_n(df: pd.DataFrame, *, n=10):
+    return df.head(n)
+
+
+@op(ENV, "Sample N")
+def sample_n(df: pd.DataFrame, *, n=10):
+    return df.sample(n)

lynxkite-app/src/lynxkite_app/crdt.py

@@ -26,11 +26,11 @@ def ws_exception_handler(exception, log):
     return True
 
 
-class WebsocketServer(pycrdt_websocket.WebsocketServer):
+class WorkspaceWebsocketServer(pycrdt_websocket.WebsocketServer):
     async def init_room(self, name: str) -> pycrdt_websocket.YRoom:
         """Initialize a room for the workspace with the given name.
 
-        The workspace is loaded from "crdt_data" if it exists there, or from "data", or a new workspace is created.
+        The workspace is loaded from ".crdt" if it exists there, or from a JSON file, or a new workspace is created.
         """
         crdt_path = pathlib.Path(".crdt")
         path = crdt_path / f"{name}.crdt"
@@ -40,9 +40,7 @@ class WebsocketServer(pycrdt_websocket.WebsocketServer):
         ydoc["workspace"] = ws = pycrdt.Map()
         # Replay updates from the store.
         try:
-            for update, timestamp in [
-                (item[0], item[-1]) async for item in ystore.read()
-            ]:
+            for update, timestamp in [(item[0], item[-1]) async for item in ystore.read()]:
                 ydoc.apply_update(update)
         except pycrdt_websocket.ystore.YDocNotFound:
             pass
@@ -84,14 +82,49 @@ class WebsocketServer(pycrdt_websocket.WebsocketServer):
         return room
 
 
+class CodeWebsocketServer(WorkspaceWebsocketServer):
+    async def init_room(self, name: str) -> pycrdt_websocket.YRoom:
+        """Initialize a room for a text document with the given name."""
+        crdt_path = pathlib.Path(".crdt")
+        path = crdt_path / f"{name}.crdt"
+        assert path.is_relative_to(crdt_path)
+        ystore = pycrdt_websocket.ystore.FileYStore(path)
+        ydoc = pycrdt.Doc()
+        ydoc["text"] = text = pycrdt.Text()
+        # Replay updates from the store.
+        try:
+            for update, timestamp in [(item[0], item[-1]) async for item in ystore.read()]:
+                ydoc.apply_update(update)
+        except pycrdt_websocket.ystore.YDocNotFound:
+            pass
+        if len(text) == 0:
+            if os.path.exists(name):
+                with open(name) as f:
+                    text += f.read()
+        room = pycrdt_websocket.YRoom(
+            ystore=ystore, ydoc=ydoc, exception_handler=ws_exception_handler
+        )
+        room.text = text
+
+        def on_change(changes):
+            asyncio.create_task(code_changed(name, changes, text))
+
+        text.observe(on_change)
+        return room
+
+
 last_ws_input = None
 
 
 def clean_input(ws_pyd):
     for node in ws_pyd.nodes:
         node.data.display = None
+        node.data.input_metadata = None
         node.data.error = None
         node.data.status = workspace.NodeStatus.done
+        for p in list(node.data.params):
+            if p.startswith("_"):
+                del node.data.params[p]
         node.position.x = 0
         node.position.y = 0
         if node.model_extra:
@@ -168,9 +201,12 @@ def try_to_load_workspace(ws: pycrdt.Map, name: str):
     """
     if os.path.exists(name):
         ws_pyd = workspace.load(name)
-        # We treat the display field as a black box, since it is a large
-        # dictionary that is meant to change as a whole.
-        crdt_update(ws, ws_pyd.model_dump(), non_collaborative_fields={"display"})
+        crdt_update(
+            ws,
+            ws_pyd.model_dump(),
+            # We treat some fields as black boxes. They are not edited on the frontend.
+            non_collaborative_fields={"display", "input_metadata"},
+        )
 
 
 last_known_versions = {}
@@ -208,9 +244,7 @@ async def workspace_changed(name: str, changes: pycrdt.MapEvent, ws_crdt: pycrdt
         await execute(name, ws_crdt, ws_pyd)
 
 
-async def execute(
-    name: str, ws_crdt: pycrdt.Map, ws_pyd: workspace.Workspace, delay: int = 0
-):
+async def execute(name: str, ws_crdt: pycrdt.Map, ws_pyd: workspace.Workspace, delay: int = 0):
     """Execute the workspace and update the CRDT object with the results.
 
     Args:
@@ -230,6 +264,7 @@ async def execute(
     assert path.is_relative_to(cwd), "Provided workspace path is invalid"
     # Save user changes before executing, in case the execution fails.
     workspace.save(ws_pyd, path)
+    ops.load_user_scripts(name)
     ws_pyd._crdt = ws_crdt
     with ws_crdt.doc.transaction():
         for nc, np in zip(ws_crdt["nodes"], ws_pyd.nodes):
@@ -243,14 +278,21 @@ async def execute(
     print(f"Finished running {name} in {ws_pyd.env}.")
 
 
+async def code_changed(name: str, changes: pycrdt.TextEvent, text: pycrdt.Text):
+    # TODO: Make this more fancy?
+    with open(name, "w") as f:
+        f.write(str(text).strip() + "\n")
+
+
 @contextlib.asynccontextmanager
 async def lifespan(app):
-    global websocket_server
-    websocket_server = WebsocketServer(
-        auto_clean_rooms=False,
-    )
-    async with websocket_server:
-        yield
+    global ws_websocket_server
+    global code_websocket_server
+    ws_websocket_server = WorkspaceWebsocketServer(auto_clean_rooms=False)
+    code_websocket_server = CodeWebsocketServer(auto_clean_rooms=False)
+    async with ws_websocket_server:
+        async with code_websocket_server:
+            yield
     print("closing websocket server")
 
 
@@ -261,5 +303,12 @@ def sanitize_path(path):
 @router.websocket("/ws/crdt/{room_name}")
 async def crdt_websocket(websocket: fastapi.WebSocket, room_name: str):
     room_name = sanitize_path(room_name)
-    server = pycrdt_websocket.ASGIServer(websocket_server)
+    server = pycrdt_websocket.ASGIServer(ws_websocket_server)
+    await server({"path": room_name}, websocket._receive, websocket._send)
+
+
+@router.websocket("/ws/code/crdt/{room_name}")
+async def code_crdt_websocket(websocket: fastapi.WebSocket, room_name: str):
+    room_name = sanitize_path(room_name)
+    server = pycrdt_websocket.ASGIServer(code_websocket_server)
     await server({"path": room_name}, websocket._receive, websocket._send)

lynxkite-app/src/lynxkite_app/main.py

@@ -26,6 +26,7 @@ def detect_plugins():
 
 
 lynxkite_plugins = detect_plugins()
+ops.save_catalogs("plugins loaded")
 
 app = fastapi.FastAPI(lifespan=crdt.lifespan)
 app.include_router(crdt.router)
@@ -33,11 +34,9 @@ app.add_middleware(GZipMiddleware)
 
 
 @app.get("/api/catalog")
-def get_catalog():
-    return {
-        k: {op.name: op.model_dump() for op in v.values()}
-        for k, v in ops.CATALOGS.items()
-    }
+def get_catalog(workspace: str):
+    ops.load_user_scripts(workspace)
+    return {k: {op.name: op.model_dump() for op in v.values()} for k, v in ops.CATALOGS.items()}
 
 
 class SaveRequest(workspace.BaseConfig):
@@ -85,6 +84,15 @@ class DirectoryEntry(pydantic.BaseModel):
     type: str
 
 
+def _get_path_type(path: pathlib.Path) -> str:
+    if path.is_dir():
+        return "directory"
+    elif path.suffixes[-2:] == [".lynxkite", ".json"]:
+        return "workspace"
+    else:
+        return "file"
+
+
 @app.get("/api/dir/list")
 def list_dir(path: str):
     path = data_path / path
@@ -93,7 +101,7 @@ def list_dir(path: str):
         [
             DirectoryEntry(
                 name=str(p.relative_to(data_path)),
-                type="directory" if p.is_dir() else "workspace",
+                type=_get_path_type(p),
             )
             for p in path.iterdir()
             if not p.name.startswith(".")

lynxkite-app/tests/test_main.py

@@ -22,7 +22,7 @@ def test_detect_plugins_with_plugins():
 
 
 def test_get_catalog():
-    response = client.get("/api/catalog")
+    response = client.get("/api/catalog?workspace=test")
     assert response.status_code == 200
 
 
@@ -37,6 +37,7 @@ def test_save_and_load():
                     "type": "basic",
                     "data": {
                         "display": None,
+                        "input_metadata": None,
                         "error": "Unknown operation.",
                         "title": "Test node",
                         "params": {"param1": "value"},
@@ -58,15 +59,22 @@ def test_save_and_load():
 def test_list_dir():
     test_dir = pathlib.Path() / str(uuid.uuid4())
     test_dir.mkdir(parents=True, exist_ok=True)
-    test_file = test_dir / "test_file.txt"
-    test_file.touch()
+    dir = test_dir / "test_dir"
+    dir.mkdir(exist_ok=True)
+    file = test_dir / "test_file.txt"
+    file.touch()
+    ws = test_dir / "test_workspace.lynxkite.json"
+    ws.touch()
     response = client.get(f"/api/dir/list?path={str(test_dir)}")
     assert response.status_code == 200
-    assert len(response.json()) == 1
-    assert response.json()[0]["name"] == f"{test_dir}/test_file.txt"
-    assert response.json()[0]["type"] == "workspace"
-    test_file.unlink()
-    test_dir.rmdir()
+    assert response.json() == [
+        {"name": f"{test_dir}/test_dir", "type": "directory"},
+        {"name": f"{test_dir}/test_file.txt", "type": "file"},
+        {"name": f"{test_dir}/test_workspace.lynxkite.json", "type": "workspace"},
+    ]
+    file.unlink()
+    ws.unlink()
+    dir.rmdir()
 
 
 def test_make_dir():

lynxkite-app/web/eslint.config.js

@@ -19,10 +19,7 @@ export default tseslint.config(
     },
     rules: {
       ...reactHooks.configs.recommended.rules,
-      "react-refresh/only-export-components": [
-        "warn",
-        { allowConstantExport: true },
-      ],
+      "react-refresh/only-export-components": ["warn", { allowConstantExport: true }],
     },
   },
 );

lynxkite-app/web/index.html

@@ -4,7 +4,6 @@
     <meta charset="UTF-8" />
     <link rel="icon" type="image/svg+xml" href="/src/assets/favicon.ico" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>LynxKite 2025</title>
   </head>
   <body>
     <div id="root"></div>

lynxkite-app/web/package-lock.json

@@ -10,6 +10,7 @@
       "dependencies": {
         "@esbuild/linux-x64": "^0.25.0",
         "@iconify-json/tabler": "^1.2.10",
+        "@monaco-editor/react": "^4.7.0",
         "@svgr/core": "^8.1.0",
         "@svgr/plugin-jsx": "^8.1.0",
         "@swc/core": "^1.10.1",
@@ -28,6 +29,7 @@
         "react-router-dom": "^7.0.2",
         "swr": "^2.2.5",
         "unplugin-icons": "^0.21.0",
+        "y-monaco": "^0.1.6",
         "y-websocket": "^2.0.4",
         "yjs": "^13.6.20"
       },
@@ -1105,6 +1107,29 @@
       "integrity": "sha512-4JQNk+3mVzK3xh2rqd6RB4J46qUR19azEHBneZyTZM+c456qOrbbM/5xcR8huNCCcbVt7+UmizG6GuUvPvKUYg==",
       "license": "MIT"
     },
+    "node_modules/@monaco-editor/loader": {
+      "version": "1.5.0",
+      "resolved": "https://registry.npmjs.org/@monaco-editor/loader/-/loader-1.5.0.tgz",
+      "integrity": "sha512-hKoGSM+7aAc7eRTRjpqAZucPmoNOC4UUbknb/VNoTkEIkCPhqV8LfbsgM1webRM7S/z21eHEx9Fkwx8Z/C/+Xw==",
+      "license": "MIT",
+      "dependencies": {
+        "state-local": "^1.0.6"
+      }
+    },
+    "node_modules/@monaco-editor/react": {
+      "version": "4.7.0",
+      "resolved": "https://registry.npmjs.org/@monaco-editor/react/-/react-4.7.0.tgz",
+      "integrity": "sha512-cyzXQCtO47ydzxpQtCGSQGOC8Gk3ZUeBXFAxD+CWXYFo5OqZyZUonFl0DwUlTyAfRHntBfw2p3w4s9R6oe1eCA==",
+      "license": "MIT",
+      "dependencies": {
+        "@monaco-editor/loader": "^1.5.0"
+      },
+      "peerDependencies": {
+        "monaco-editor": ">= 0.25.0 < 1",
+        "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0",
+        "react-dom": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0"
+      }
+    },
     "node_modules/@nodelib/fs.scandir": {
       "version": "2.1.5",
       "resolved": "https://registry.npmjs.org/@nodelib/fs.scandir/-/fs.scandir-2.1.5.tgz",
@@ -5436,6 +5461,13 @@
         "ufo": "^1.5.4"
       }
     },
+    "node_modules/monaco-editor": {
+      "version": "0.52.2",
+      "resolved": "https://registry.npmjs.org/monaco-editor/-/monaco-editor-0.52.2.tgz",
+      "integrity": "sha512-GEQWEZmfkOGLdd3XK8ryrfWz3AIP8YymVXiPHEdewrUq7mh0qrKrfHLNCXcbB6sTnMLnOZ3ztSiKcciFUkIJwQ==",
+      "license": "MIT",
+      "peer": true
+    },
     "node_modules/ms": {
       "version": "2.1.3",
       "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz",
@@ -6437,6 +6469,12 @@
         "url": "https://github.com/sponsors/wooorm"
       }
     },
+    "node_modules/state-local": {
+      "version": "1.0.7",
+      "resolved": "https://registry.npmjs.org/state-local/-/state-local-1.0.7.tgz",
+      "integrity": "sha512-HTEHMNieakEnoe33shBYcZ7NX83ACUjCu8c40iOGEZsngj9zRnkqS9j1pqQPXwobB0ZcVTk27REb7COQ0UR59w==",
+      "license": "MIT"
+    },
     "node_modules/string_decoder": {
       "version": "1.3.0",
       "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz",
@@ -7360,6 +7398,23 @@
         "yjs": "^13.0.0"
       }
     },
+    "node_modules/y-monaco": {
+      "version": "0.1.6",
+      "resolved": "https://registry.npmjs.org/y-monaco/-/y-monaco-0.1.6.tgz",
+      "integrity": "sha512-sYRywMmcylt+Nupl+11AvizD2am06ST8lkVbUXuaEmrtV6Tf+TD4rsEm6u9YGGowYue+Vfg1IJ97SUP2J+PVXg==",
+      "license": "MIT",
+      "dependencies": {
+        "lib0": "^0.2.43"
+      },
+      "engines": {
+        "node": ">=12.0.0",
+        "npm": ">=6.0.0"
+      },
+      "peerDependencies": {
+        "monaco-editor": ">=0.20.0",
+        "yjs": "^13.3.1"
+      }
+    },
     "node_modules/y-protocols": {
       "version": "1.0.6",
       "resolved": "https://registry.npmjs.org/y-protocols/-/y-protocols-1.0.6.tgz",

lynxkite-app/web/package.json

@@ -13,6 +13,7 @@
   "dependencies": {
     "@esbuild/linux-x64": "^0.25.0",
     "@iconify-json/tabler": "^1.2.10",
+    "@monaco-editor/react": "^4.7.0",
     "@svgr/core": "^8.1.0",
     "@svgr/plugin-jsx": "^8.1.0",
     "@swc/core": "^1.10.1",
@@ -31,6 +32,7 @@
     "react-router-dom": "^7.0.2",
     "swr": "^2.2.5",
     "unplugin-icons": "^0.21.0",
+    "y-monaco": "^0.1.6",
     "y-websocket": "^2.0.4",
     "yjs": "^13.6.20"
   },

lynxkite-app/web/playwright.config.ts

@@ -7,6 +7,7 @@ export default defineConfig({
   /* Fail the build on CI if you accidentally left test.only in the source code. */
   forbidOnly: !!process.env.CI,
   retries: process.env.CI ? 1 : 0,
+  maxFailures: 5,
   workers: 1,
   reporter: process.env.CI ? [["github"], ["html"]] : "html",
   use: {
@@ -24,7 +25,7 @@ export default defineConfig({
   ],
   webServer: {
     command: "cd ../../examples && lynxkite",
-    url: "http://127.0.0.1:8000",
+    port: 8000,
     reuseExistingServer: false,
   },
 });

lynxkite-app/web/src/Code.tsx

@@ -0,0 +1,101 @@
+// Full-page editor for code files.
+
+import Editor, { type Monaco } from "@monaco-editor/react";
+import type { editor } from "monaco-editor";
+import { useEffect, useRef } from "react";
+import { useParams } from "react-router";
+import { WebsocketProvider } from "y-websocket";
+import * as Y from "yjs";
+// @ts-ignore
+import Atom from "~icons/tabler/atom.jsx";
+// @ts-ignore
+import Backspace from "~icons/tabler/backspace.jsx";
+// @ts-ignore
+import Close from "~icons/tabler/x.jsx";
+import favicon from "./assets/favicon.ico";
+import theme from "./code-theme.ts";
+
+export default function Code() {
+  const { path } = useParams();
+  const parentDir = path!.split("/").slice(0, -1).join("/");
+  const yDocRef = useRef<any>();
+  const wsProviderRef = useRef<any>();
+  const monacoBindingRef = useRef<any>();
+  const yMonacoRef = useRef<any>();
+  const editorRef = useRef<any>();
+  useEffect(() => {
+    const loadMonaco = async () => {
+      // y-monaco is gigantic. The other Monaco packages are small.
+      yMonacoRef.current = await import("y-monaco");
+      initCRDT();
+    };
+    loadMonaco();
+  }, []);
+  function beforeMount(monaco: Monaco) {
+    monaco.editor.defineTheme("lynxkite", theme);
+  }
+  function onMount(_editor: editor.IStandaloneCodeEditor) {
+    editorRef.current = _editor;
+    initCRDT();
+  }
+  function initCRDT() {
+    if (!yMonacoRef.current || !editorRef.current) return;
+    if (yDocRef.current) return;
+    yDocRef.current = new Y.Doc();
+    const text = yDocRef.current.getText("text");
+    const proto = location.protocol === "https:" ? "wss:" : "ws:";
+    wsProviderRef.current = new WebsocketProvider(
+      `${proto}//${location.host}/ws/code/crdt`,
+      path!,
+      yDocRef.current,
+    );
+    monacoBindingRef.current = new yMonacoRef.current.MonacoBinding(
+      text,
+      editorRef.current.getModel()!,
+      new Set([editorRef.current]),
+      wsProviderRef.current.awareness,
+    );
+  }
+  useEffect(() => {
+    return () => {
+      yDocRef.current?.destroy();
+      wsProviderRef.current?.destroy();
+      monacoBindingRef.current?.destroy();
+    };
+  });
+  return (
+    <div className="workspace">
+      <div className="top-bar bg-neutral">
+        <a className="logo" href="">
+          <img alt="" src={favicon} />
+        </a>
+        <div className="ws-name">{path}</div>
+        <div className="tools text-secondary">
+          <a href="">
+            <Atom />
+          </a>
+          <a href="">
+            <Backspace />
+          </a>
+          <a href={`/dir/${parentDir}`}>
+            <Close />
+          </a>
+        </div>
+      </div>
+      <Editor
+        defaultLanguage="python"
+        theme="lynxkite"
+        path={path}
+        beforeMount={beforeMount}
+        onMount={onMount}
+        loading={null}
+        options={{
+          cursorStyle: "block",
+          cursorBlinking: "solid",
+          minimap: { enabled: false },
+          renderLineHighlight: "none",
+        }}
+      />
+    </div>
+  );
+}

lynxkite-app/web/src/Directory.tsx

@@ -15,9 +15,46 @@ import FolderPlus from "~icons/tabler/folder-plus";
 // @ts-ignore
 import Home from "~icons/tabler/home";
 // @ts-ignore
+import LayoutGrid from "~icons/tabler/layout-grid";
+// @ts-ignore
+import LayoutGridAdd from "~icons/tabler/layout-grid-add";
+// @ts-ignore
 import Trash from "~icons/tabler/trash";
 import logo from "./assets/logo.png";
 
+function EntryCreator(props: {
+  label: string;
+  icon: JSX.Element;
+  onCreate: (name: string) => void;
+}) {
+  const [isCreating, setIsCreating] = useState(false);
+  return (
+    <>
+      {isCreating ? (
+        <form
+          onSubmit={(e) => {
+            e.preventDefault();
+            props.onCreate((e.target as HTMLFormElement).entryName.value.trim());
+          }}
+        >
+          <input
+            className="input input-ghost w-full"
+            autoFocus
+            type="text"
+            name="entryName"
+            onBlur={() => setIsCreating(false)}
+            placeholder={`${props.label} name`}
+          />
+        </form>
+      ) : (
+        <button type="button" onClick={() => setIsCreating(true)}>
+          {props.icon} {props.label}
+        </button>
+      )}
+    </>
+  );
+}
+
 const fetcher = (url: string) => fetch(url).then((res) => res.json());
 
 export default function () {
@@ -27,68 +64,51 @@ export default function () {
     dedupingInterval: 0,
   });
   const navigate = useNavigate();
-  const [isCreatingDir, setIsCreatingDir] = useState(false);
-  const [isCreatingWorkspace, setIsCreatingWorkspace] = useState(false);
 
   function link(item: DirectoryEntry) {
     if (item.type === "directory") {
       return `/dir/${item.name}`;
     }
-    return `/edit/${item.name}`;
+    if (item.type === "workspace") {
+      return `/edit/${item.name}`;
+    }
+    return `/code/${item.name}`;
   }
 
   function shortName(item: DirectoryEntry) {
-    return item.name.split("/").pop();
+    return item.name
+      .split("/")
+      .pop()
+      ?.replace(/[.]lynxkite[.]json$/, "");
   }
 
-  function newName(list: DirectoryEntry[], baseName = "Untitled") {
-    let i = 0;
-    while (true) {
-      const name = `${baseName}${i ? ` ${i}` : ""}`;
-      if (!list.find((item) => item.name === name)) {
-        return name;
-      }
-      i++;
-    }
+  function newWorkspaceIn(path: string, workspaceName: string) {
+    const pathSlash = path ? `${path}/` : "";
+    navigate(`/edit/${pathSlash}${workspaceName}.lynxkite.json`, { replace: true });
   }
-
-  function newWorkspaceIn(
-    path: string,
-    list: DirectoryEntry[],
-    workspaceName?: string,
-  ) {
+  function newCodeFile(path: string, name: string) {
     const pathSlash = path ? `${path}/` : "";
-    const name = workspaceName || newName(list);
-    navigate(`/edit/${pathSlash}${name}`, { replace: true });
+    navigate(`/code/${pathSlash}${name}`, { replace: true });
   }
-
-  async function newFolderIn(
-    path: string,
-    list: DirectoryEntry[],
-    folderName?: string,
-  ) {
-    const name = folderName || newName(list, "New Folder");
+  async function newFolderIn(path: string, folderName: string) {
     const pathSlash = path ? `${path}/` : "";
-
     const res = await fetch("/api/dir/mkdir", {
       method: "POST",
       headers: { "Content-Type": "application/json" },
-      body: JSON.stringify({ path: pathSlash + name }),
+      body: JSON.stringify({ path: pathSlash + folderName }),
     });
     if (res.ok) {
-      navigate(`/dir/${pathSlash}${name}`);
+      navigate(`/dir/${pathSlash}${folderName}`);
     } else {
       alert("Failed to create folder.");
     }
   }
 
   async function deleteItem(item: DirectoryEntry) {
-    if (!window.confirm(`Are you sure you want to delete "${item.name}"?`))
-      return;
+    if (!window.confirm(`Are you sure you want to delete "${item.name}"?`)) return;
     const pathSlash = path ? `${path}/` : "";
 
-    const apiPath =
-      item.type === "directory" ? "/api/dir/delete" : "/api/delete";
+    const apiPath = item.type === "directory" ? "/api/dir/delete" : "/api/delete";
     await fetch(apiPath, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
@@ -115,89 +135,66 @@ export default function () {
         {list.data && (
           <>
             <div className="actions">
-              <div className="new-workspace">
-                {isCreatingWorkspace && (
-                  // @ts-ignore
-                  <form
-                    onSubmit={(e) => {
-                      e.preventDefault();
-                      newWorkspaceIn(
-                        path || "",
-                        list.data,
-                        (
-                          e.target as HTMLFormElement
-                        ).workspaceName.value.trim(),
-                      );
-                    }}
-                  >
-                    <input
-                      type="text"
-                      name="workspaceName"
-                      defaultValue={newName(list.data)}
-                      placeholder={newName(list.data)}
-                    />
-                  </form>
-                )}
-                <button
-                  type="button"
-                  onClick={() => setIsCreatingWorkspace(true)}
-                >
-                  <FolderPlus /> New workspace
-                </button>
-              </div>
-
-              <div className="new-folder">
-                {isCreatingDir && (
-                  // @ts-ignore
-                  <form
-                    onSubmit={(e) => {
-                      e.preventDefault();
-                      newFolderIn(
-                        path || "",
-                        list.data,
-                        (e.target as HTMLFormElement).folderName.value.trim(),
-                      );
-                    }}
-                  >
-                    <input
-                      type="text"
-                      name="folderName"
-                      defaultValue={newName(list.data)}
-                      placeholder={newName(list.data)}
-                    />
-                  </form>
-                )}
-                <button type="button" onClick={() => setIsCreatingDir(true)}>
-                  <FolderPlus /> New folder
-                </button>
-              </div>
+              <EntryCreator
+                onCreate={(name) => {
+                  newWorkspaceIn(path || "", name);
+                }}
+                icon={<LayoutGridAdd />}
+                label="New workspace"
+              />
+              <EntryCreator
+                onCreate={(name) => {
+                  newCodeFile(path || "", name);
+                }}
+                icon={<FilePlus />}
+                label="New code file"
+              />
+              <EntryCreator
+                onCreate={(name: string) => {
+                  newFolderIn(path || "", name);
+                }}
+                icon={<FolderPlus />}
+                label="New folder"
+              />
             </div>
 
-            {path && (
+            {path ? (
               <div className="breadcrumbs">
                 <Link to="/dir/">
                   <Home />
                 </Link>{" "}
                 <span className="current-folder">{path}</span>
+                <title>{path}</title>
               </div>
+            ) : (
+              <title>LynxKite 2000:MM</title>
             )}
 
-            {list.data.map((item: DirectoryEntry) => (
-              <div key={item.name} className="entry">
-                <Link key={link(item)} to={link(item)}>
-                  {item.type === "directory" ? <Folder /> : <File />}
-                  {shortName(item)}
-                </Link>
-                <button
-                  type="button"
-                  onClick={() => {
-                    deleteItem(item);
-                  }}
-                >
-                  <Trash />
-                </button>
-              </div>
-            ))}
+            {list.data.map(
+              (item: DirectoryEntry) =>
+                !shortName(item)?.startsWith("__") && (
+                  <div key={item.name} className="entry">
+                    <Link key={link(item)} to={link(item)}>
+                      {item.type === "directory" ? (
+                        <Folder />
+                      ) : item.type === "workspace" ? (
+                        <LayoutGrid />
+                      ) : (
+                        <File />
+                      )}
+                      {shortName(item)}
+                    </Link>
+                    <button
+                      type="button"
+                      onClick={() => {
+                        deleteItem(item);
+                      }}
+                    >
+                      <Trash />
+                    </button>
+                  </div>
+                ),
+            )}
           </>
         )}
       </div>{" "}

lynxkite-app/web/src/apiTypes.ts

@@ -5,6 +5,8 @@
 /* Do not modify it by hand - just update the pydantic models and then re-run the script
 */
 
+export type NodeStatus = "planned" | "active" | "done";
+
 export interface DirectoryEntry {
   name: string;
   type: string;
@@ -40,8 +42,9 @@ export interface WorkspaceNodeData {
     [k: string]: unknown;
   };
   display?: unknown;
+  input_metadata?: unknown;
   error?: string | null;
-  in_progress?: boolean;
+  status?: NodeStatus;
   [k: string]: unknown;
 }
 export interface Position {

lynxkite-app/web/src/code-theme.ts

@@ -0,0 +1,38 @@
+// A simple theme using the LynxKite colors.
+
+import type { editor } from "monaco-editor/esm/vs/editor/editor.api";
+
+const theme: editor.IStandaloneThemeData = {
+  base: "vs-dark",
+  inherit: true,
+  rules: [
+    {
+      foreground: "ff8800",
+      token: "keyword",
+    },
+    {
+      foreground: "0088ff",
+      fontStyle: "italic",
+      token: "comment",
+    },
+    {
+      foreground: "39bcf3",
+      token: "string",
+    },
+    {
+      foreground: "ffc600",
+      token: "",
+    },
+  ],
+  colors: {
+    "editor.foreground": "#FFFFFF",
+    "editor.background": "#002a4c",
+    "editor.selectionBackground": "#0050a4",
+    "editor.lineHighlightBackground": "#1f4662",
+    "editorCursor.foreground": "#ffc600",
+    "editorWhitespace.foreground": "#7f7f7fb2",
+    "editorIndentGuide.background": "#3b5364",
+    "editorIndentGuide.activeBackground": "#ffc600",
+  },
+};
+export default theme;

lynxkite-app/web/src/index.css

@@ -102,15 +102,14 @@ body {
     --status-color-1: oklch(75% 0.2 55);
     --status-color-2: oklch(75% 0.2 55);
     --status-color-3: oklch(75% 0.2 55);
-    transition: --status-color-1 0.3s, --status-color-2 0.3s, --status-color-3
-      0.3s;
+    transition: --status-color-1 0.3s, --status-color-2 0.3s, --status-color-3 0.3s;
   }
 
   .lynxkite-node .title.active {
     --status-color-1: oklch(75% 0.2 55);
     --status-color-2: oklch(90% 0.2 55);
     --status-color-3: oklch(75% 0.1 55);
-    /* animation: active-node-gradient-animation 2s ease-in-out infinite; */
+    animation: active-node-gradient-animation 2s ease-in-out infinite;
   }
 
   .lynxkite-node .title.planned {
@@ -256,6 +255,14 @@ body {
       cursor: pointer;
     }
   }
+
+  .model-mapping-param {
+    border: 1px solid var(--fallback-bc, oklch(var(--bc) / 0.2));
+    border-collapse: separate;
+    border-radius: 5px;
+    padding: 5px 10px;
+    width: 100%;
+  }
 }
 
 .params-expander {
@@ -319,7 +326,14 @@ body {
   .actions {
     display: flex;
     justify-content: space-evenly;
+    align-items: center;
+    height: 50px;
     padding: 5px;
+
+    form,
+    button {
+      flex: 1;
+    }
   }
 
   .actions a {
@@ -527,3 +541,25 @@ body {
 .add-relationship-button:hover {
   background-color: #218838;
 }
+
+.yRemoteSelection {
+  background-color: rgb(250, 129, 0, 0.5);
+}
+
+.yRemoteSelectionHead {
+  position: absolute;
+  border-left: #ff8800 solid 2px;
+  border-top: #ff8800 solid 2px;
+  border-bottom: #ff8800 solid 2px;
+  height: 100%;
+  box-sizing: border-box;
+}
+
+.yRemoteSelectionHead::after {
+  position: absolute;
+  content: " ";
+  border: 3px solid #ff8800;
+  border-radius: 4px;
+  left: -4px;
+  top: -5px;
+}

lynxkite-app/web/src/main.tsx

@@ -3,6 +3,7 @@ import { createRoot } from "react-dom/client";
 import "@xyflow/react/dist/style.css";
 import "./index.css";
 import { BrowserRouter, Route, Routes } from "react-router";
+import Code from "./Code.tsx";
 import Directory from "./Directory.tsx";
 import Workspace from "./workspace/Workspace.tsx";
 
@@ -14,6 +15,7 @@ createRoot(document.getElementById("root")!).render(
         <Route path="/dir" element={<Directory />} />
         <Route path="/dir/:path" element={<Directory />} />
         <Route path="/edit/:path" element={<Workspace />} />
+        <Route path="/code/:path" element={<Code />} />
       </Routes>
     </BrowserRouter>
   </StrictMode>,

lynxkite-app/web/src/workspace/NodeSearch.tsx

@@ -30,9 +30,7 @@ export default function (props: {
     boxes.sort((a, b) => a.item.name.localeCompare(b.item.name));
     return boxes;
   }, [props.boxes]);
-  const hits: { item: OpsOp }[] = searchText
-    ? fuse.search<OpsOp>(searchText)
-    : allOps;
+  const hits: { item: OpsOp }[] = searchText ? fuse.search<OpsOp>(searchText) : allOps;
   const [selectedIndex, setSelectedIndex] = useState(0);
   useEffect(() => searchBox.current.focus());
   function typed(text: string) {
@@ -64,10 +62,7 @@ export default function (props: {
   }
 
   return (
-    <div
-      className="node-search"
-      style={{ top: props.pos.y, left: props.pos.x }}
-    >
+    <div className="node-search" style={{ top: props.pos.y, left: props.pos.x }}>
       <input
         ref={searchBox}
         value={searchText}

lynxkite-app/web/src/workspace/Workspace.tsx

@@ -1,3 +1,5 @@
+// The LynxKite workspace editor.
+
 import { getYjsDoc, syncedStore } from "@syncedstore/core";
 import {
   type Connection,
@@ -15,14 +17,7 @@ import {
   useUpdateNodeInternals,
 } from "@xyflow/react";
 import axios from "axios";
-import {
-  type MouseEvent,
-  useCallback,
-  useEffect,
-  useMemo,
-  useState,
-} from "react";
-// The LynxKite workspace editor.
+import { type MouseEvent, useCallback, useEffect, useMemo, useState } from "react";
 import { useParams } from "react-router";
 import useSWR, { type Fetcher } from "swr";
 import { WebsocketProvider } from "y-websocket";
@@ -37,11 +32,7 @@ import favicon from "../assets/favicon.ico";
 // import NodeWithTableView from './NodeWithTableView';
 import EnvironmentSelector from "./EnvironmentSelector";
 import { LynxKiteState } from "./LynxKiteState";
-import NodeSearch, {
-  type OpsOp,
-  type Catalog,
-  type Catalogs,
-} from "./NodeSearch.tsx";
+import NodeSearch, { type OpsOp, type Catalog, type Catalogs } from "./NodeSearch.tsx";
 import NodeWithGraphCreationView from "./nodes/GraphCreationNode.tsx";
 import NodeWithImage from "./nodes/NodeWithImage.tsx";
 import NodeWithParams from "./nodes/NodeWithParams";
@@ -62,6 +53,10 @@ function LynxKiteFlow() {
   const [nodes, setNodes] = useState([] as Node[]);
   const [edges, setEdges] = useState([] as Edge[]);
   const { path } = useParams();
+  const shortPath = path!
+    .split("/")
+    .pop()!
+    .replace(/[.]lynxkite[.]json$/, "");
   const [state, setState] = useState({ workspace: {} as Workspace });
   const [message, setMessage] = useState(null as string | null);
   useEffect(() => {
@@ -69,11 +64,7 @@ function LynxKiteFlow() {
     setState(state);
     const doc = getYjsDoc(state);
     const proto = location.protocol === "https:" ? "wss:" : "ws:";
-    const wsProvider = new WebsocketProvider(
-      `${proto}//${location.host}/ws/crdt`,
-      path!,
-      doc,
-    );
+    const wsProvider = new WebsocketProvider(`${proto}//${location.host}/ws/crdt`, path!, doc);
     const onChange = (_update: any, origin: any, _doc: any, _tr: any) => {
       if (origin === wsProvider) {
         // An update from the CRDT. Apply it to the local state.
@@ -165,7 +156,7 @@ function LynxKiteFlow() {
 
   const fetcher: Fetcher<Catalogs> = (resource: string, init?: RequestInit) =>
     fetch(resource, init).then((res) => res.json());
-  const catalog = useSWR("/api/catalog", fetcher);
+  const catalog = useSWR(`/api/catalog?workspace=${path}`, fetcher);
   const [suppressSearchUntil, setSuppressSearchUntil] = useState(0);
   const [nodeSearchSettings, setNodeSearchSettings] = useState(
     undefined as
@@ -190,11 +181,7 @@ function LynxKiteFlow() {
   useEffect(() => {
     const handleKeyDown = (event: KeyboardEvent) => {
       // Show the node search dialog on "/".
-      if (
-        event.key === "/" &&
-        !nodeSearchSettings &&
-        !isTypingInFormElement()
-      ) {
+      if (event.key === "/" && !nodeSearchSettings && !isTypingInFormElement()) {
         event.preventDefault();
         setNodeSearchSettings({
           pos: { x: 100, y: 100 },
@@ -238,11 +225,7 @@ function LynxKiteFlow() {
     },
     [catalog, state, nodeSearchSettings, suppressSearchUntil, closeNodeSearch],
   );
-  function addNode(
-    node: Partial<WorkspaceNode>,
-    state: { workspace: Workspace },
-    nodes: Node[],
-  ) {
+  function addNode(node: Partial<WorkspaceNode>, state: { workspace: Workspace }, nodes: Node[]) {
     const title = node.data?.title;
     let i = 1;
     node.id = `${title} ${i}`;
@@ -260,9 +243,7 @@ function LynxKiteFlow() {
       data: {
         meta: meta,
         title: meta.name,
-        params: Object.fromEntries(
-          Object.values(meta.params).map((p) => [p.name, p.default]),
-        ),
+        params: Object.fromEntries(Object.values(meta.params).map((p) => [p.name, p.default])),
       },
     };
     return node;
@@ -310,9 +291,7 @@ function LynxKiteFlow() {
     try {
       await axios.post("/api/upload", formData, {
         onUploadProgress: (progressEvent) => {
-          const percentCompleted = Math.round(
-            (100 * progressEvent.loaded) / progressEvent.total!,
-          );
+          const percentCompleted = Math.round((100 * progressEvent.loaded) / progressEvent.total!);
           if (percentCompleted === 100) setMessage("Processing file...");
           else setMessage(`Uploading ${percentCompleted}%`);
         },
@@ -345,7 +324,8 @@ function LynxKiteFlow() {
         <a className="logo" href="">
           <img alt="" src={favicon} />
         </a>
-        <div className="ws-name">{path}</div>
+        <div className="ws-name">{shortPath}</div>
+        <title>{shortPath}</title>
         <EnvironmentSelector
           options={Object.keys(catalog.data || {})}
           value={state.workspace.env!}
@@ -365,11 +345,7 @@ function LynxKiteFlow() {
           </a>
         </div>
       </div>
-      <div
-        style={{ height: "100%", width: "100vw" }}
-        onDragOver={onDragOver}
-        onDrop={onDrop}
-      >
+      <div style={{ height: "100%", width: "100vw" }} onDragOver={onDragOver} onDrop={onDrop}>
         <LynxKiteState.Provider value={state}>
           <ReactFlow
             nodes={nodes}
@@ -382,7 +358,9 @@ function LynxKiteFlow() {
             onConnect={onConnect}
             proOptions={{ hideAttribution: true }}
             maxZoom={1}
-            minZoom={0.3}
+            minZoom={0.2}
+            zoomOnScroll={false}
+            preventScrolling={false}
             defaultEdgeOptions={{
               markerEnd: {
                 type: MarkerType.ArrowClosed,

lynxkite-app/web/src/workspace/nodes/GraphCreationNode.tsx

@@ -20,12 +20,7 @@ function toMD(v: any): string {
 function displayTable(name: string, df: any) {
   if (df.data.length > 1) {
     return (
-      <Table
-        key={`${name}-table`}
-        name={`${name}-table`}
-        columns={df.columns}
-        data={df.data}
-      />
+      <Table key={`${name}-table`} name={`${name}-table`} columns={df.columns} data={df.data} />
     );
   }
   if (df.data.length) {
@@ -60,9 +55,7 @@ export default function NodeWithGraphCreationView(props: any) {
   const display = props.data.display?.value;
   const tables = display?.dataframes || {};
   const singleTable = tables && Object.keys(tables).length === 1;
-  const [relations, setRelations] = useState(
-    relationsToDict(display?.relations) || {},
-  );
+  const [relations, setRelations] = useState(relationsToDict(display?.relations) || {});
   const singleRelation = relations && Object.keys(relations).length === 1;
   function setParam(name: string, newValue: any, opts: UpdateOptions) {
     reactFlow.updateNodeData(props.id, {
@@ -211,9 +204,7 @@ export default function NodeWithGraphCreationView(props: any) {
 
         <datalist id="edges-column-options">
           {tables[relation.source_table] &&
-            tables[relation.df].columns.map((name: string) => (
-              <option key={name} value={name} />
-            ))}
+            tables[relation.df].columns.map((name: string) => <option key={name} value={name} />)}
         </datalist>
 
         <datalist id="source-node-column-options">
@@ -274,10 +265,7 @@ export default function NodeWithGraphCreationView(props: any) {
         <div className="graph-relations">
           <div className="graph-table-header">
             Relationships
-            <button
-              className="add-relationship-button"
-              onClick={(_) => addRelation()}
-            >
+            <button className="add-relationship-button" onClick={(_) => addRelation()}>
               +
             </button>
           </div>

lynxkite-app/web/src/workspace/nodes/LynxKiteNode.tsx

@@ -1,9 +1,4 @@
-import {
-  Handle,
-  NodeResizeControl,
-  type Position,
-  useReactFlow,
-} from "@xyflow/react";
+import { Handle, NodeResizeControl, type Position, useReactFlow } from "@xyflow/react";
 // @ts-ignore
 import ChevronDownRight from "~icons/tabler/chevron-down-right.jsx";
 
@@ -38,10 +33,8 @@ function getHandles(inputs: object, outputs: object) {
   }
   for (const e of handles) {
     e.offsetPercentage = (100 * (e.index + 1)) / (counts[e.position] + 1);
-    const simpleHorizontal =
-      counts.top === 0 && counts.bottom === 0 && handles.length <= 2;
-    const simpleVertical =
-      counts.left === 0 && counts.right === 0 && handles.length <= 2;
+    const simpleHorizontal = counts.top === 0 && counts.bottom === 0 && handles.length <= 2;
+    const simpleVertical = counts.left === 0 && counts.right === 0 && handles.length <= 2;
     e.showLabel = !simpleHorizontal && !simpleVertical;
   }
   return handles;
@@ -71,10 +64,7 @@ export default function LynxKiteNode(props: LynxKiteNodeProps) {
       }}
     >
       <div className="lynxkite-node" style={props.nodeStyle}>
-        <div
-          className={`title bg-primary ${data.status}`}
-          onClick={titleClicked}
-        >
+        <div className={`title bg-primary ${data.status}`} onClick={titleClicked}>
           {data.title}
           {data.error && <span className="title-icon">⚠️</span>}
           {expanded || <span className="title-icon">⋯</span>}
@@ -99,14 +89,11 @@ export default function LynxKiteNode(props: LynxKiteNodeProps) {
             type={handle.type}
             position={handle.position as Position}
             style={{
-              [handleOffsetDirection[handle.position]]:
-                `${handle.offsetPercentage}% `,
+              [handleOffsetDirection[handle.position]]: `${handle.offsetPercentage}% `,
             }}
           >
             {handle.showLabel && (
-              <span className="handle-name">
-                {handle.name.replace(/_/g, " ")}
-              </span>
+              <span className="handle-name">{handle.name.replace(/_/g, " ")}</span>
             )}
           </Handle>
         ))}

lynxkite-app/web/src/workspace/nodes/NodeGroupParameter.tsx

@@ -24,6 +24,7 @@ interface GroupsType {
 interface NodeGroupParameterProps {
   meta: { selector: SelectorType; groups: GroupsType };
   value: any;
+  data: any;
   setParam: (name: string, value: any, options?: { delay: number }) => void;
   deleteParam: (name: string, options?: { delay: number }) => void;
 }
@@ -31,14 +32,13 @@ interface NodeGroupParameterProps {
 export default function NodeGroupParameter({
   meta,
   value,
+  data,
   setParam,
   deleteParam,
 }: NodeGroupParameterProps) {
   const selector = meta.selector;
   const groups = meta.groups;
-  const [selectedValue, setSelectedValue] = useState<string>(
-    value || selector.default,
-  );
+  const [selectedValue, setSelectedValue] = useState<string>(value || selector.default);
 
   const handleSelectorChange = (value: any, opts?: { delay: number }) => {
     setSelectedValue(value);
@@ -47,9 +47,7 @@ export default function NodeGroupParameter({
 
   useEffect(() => {
     // Clean possible previous parameters first
-    Object.values(groups).flatMap((group) =>
-      group.map((entry) => deleteParam(entry.name)),
-    );
+    Object.values(groups).flatMap((group) => group.map((entry) => deleteParam(entry.name)));
     for (const param of groups[selectedValue]) {
       setParam(param.name, param.default);
     }
@@ -60,6 +58,7 @@ export default function NodeGroupParameter({
       name={selector.name}
       key={selector.name}
       value={selectedValue}
+      data={data}
       meta={selector}
       onChange={handleSelectorChange}
     />

lynxkite-app/web/src/workspace/nodes/NodeParameter.tsx

@@ -1,8 +1,186 @@
-const BOOLEAN = "<class 'bool'>";
+import { useRef } from "react";
+// @ts-ignore
+import ArrowsHorizontal from "~icons/tabler/arrows-horizontal.jsx";
 
+const BOOLEAN = "<class 'bool'>";
+const MODEL_TRAINING_INPUT_MAPPING =
+  "<class 'lynxkite_graph_analytics.ml_ops.ModelTrainingInputMapping'>";
+const MODEL_INFERENCE_INPUT_MAPPING =
+  "<class 'lynxkite_graph_analytics.ml_ops.ModelInferenceInputMapping'>";
+const MODEL_OUTPUT_MAPPING = "<class 'lynxkite_graph_analytics.ml_ops.ModelOutputMapping'>";
 function ParamName({ name }: { name: string }) {
+  return <span className="param-name bg-base-200">{name.replace(/_/g, " ")}</span>;
+}
+
+function Input({
+  value,
+  onChange,
+  inputRef,
+}: {
+  value: string;
+  onChange: (value: string, options?: { delay: number }) => void;
+  inputRef?: React.Ref<HTMLInputElement>;
+}) {
+  return (
+    <input
+      className="input input-bordered w-full"
+      ref={inputRef}
+      value={value ?? ""}
+      onChange={(evt) => onChange(evt.currentTarget.value, { delay: 2 })}
+      onBlur={(evt) => onChange(evt.currentTarget.value, { delay: 0 })}
+      onKeyDown={(evt) => evt.code === "Enter" && onChange(evt.currentTarget.value, { delay: 0 })}
+    />
+  );
+}
+
+type Bindings = {
+  [key: string]: {
+    df: string;
+    column: string;
+  };
+};
+
+function getModelBindings(
+  data: any,
+  variant: "training input" | "inference input" | "output",
+): string[] {
+  function bindingsOfModel(m: any): string[] {
+    switch (variant) {
+      case "training input":
+        return [...m.inputs, ...m.loss_inputs.filter((i: string) => !m.outputs.includes(i))];
+      case "inference input":
+        return m.inputs;
+      case "output":
+        return m.outputs;
+    }
+  }
+  const bindings = new Set<string>();
+  const inputs = data?.input_metadata?.value ?? data?.input_metadata ?? [];
+  for (const input of inputs) {
+    const other = input.other ?? {};
+    for (const e of Object.values(other) as any[]) {
+      if (e.type === "model") {
+        for (const b of bindingsOfModel(e.model)) {
+          bindings.add(b);
+        }
+      }
+    }
+  }
+  const list = [...bindings];
+  list.sort();
+  return list;
+}
+
+function parseJsonOrEmpty(json: string): object {
+  try {
+    const j = JSON.parse(json);
+    if (j !== null && typeof j === "object") {
+      return j;
+    }
+  } catch (e) {}
+  return {};
+}
+
+function ModelMapping({ value, onChange, data, variant }: any) {
+  const dfsRef = useRef({} as { [binding: string]: HTMLSelectElement | null });
+  const columnsRef = useRef(
+    {} as { [binding: string]: HTMLSelectElement | HTMLInputElement | null },
+  );
+  const v: any = parseJsonOrEmpty(value);
+  v.map ??= {};
+  const dfs: { [df: string]: string[] } = {};
+  const inputs = data?.input_metadata?.value ?? data?.input_metadata ?? [];
+  for (const input of inputs) {
+    if (!input.dataframes) continue;
+    const dataframes = input.dataframes as {
+      [df: string]: { columns: string[] };
+    };
+    for (const [df, { columns }] of Object.entries(dataframes)) {
+      dfs[df] = columns;
+    }
+  }
+  const bindings = getModelBindings(data, variant);
+  function getMap() {
+    const map: Bindings = {};
+    for (const binding of bindings) {
+      const df = dfsRef.current[binding]?.value ?? "";
+      const column = columnsRef.current[binding]?.value ?? "";
+      if (df.length || column.length) {
+        map[binding] = { df, column };
+      }
+    }
+    return map;
+  }
   return (
-    <span className="param-name bg-base-200">{name.replace(/_/g, " ")}</span>
+    <table className="model-mapping-param">
+      <tbody>
+        {bindings.length > 0 ? (
+          bindings.map((binding: string) => (
+            <tr key={binding}>
+              <td>{binding}</td>
+              <td>
+                <ArrowsHorizontal />
+              </td>
+              <td>
+                <select
+                  className="select select-ghost"
+                  value={v.map?.[binding]?.df}
+                  ref={(el) => {
+                    dfsRef.current[binding] = el;
+                  }}
+                  onChange={() => onChange(JSON.stringify({ map: getMap() }))}
+                >
+                  <option key="" value="" />
+                  {Object.keys(dfs).map((df: string) => (
+                    <option key={df} value={df}>
+                      {df}
+                    </option>
+                  ))}
+                </select>
+              </td>
+              <td>
+                {variant === "output" ? (
+                  <Input
+                    inputRef={(el) => {
+                      columnsRef.current[binding] = el;
+                    }}
+                    value={v.map?.[binding]?.column}
+                    onChange={(column, options) => {
+                      const map = getMap();
+                      // At this point the <input> has not been updated yet. We use the value from the event.
+                      const df = dfsRef.current[binding]?.value ?? "";
+                      map[binding] ??= { df, column };
+                      map[binding].column = column;
+                      onChange(JSON.stringify({ map }), options);
+                    }}
+                  />
+                ) : (
+                  <select
+                    className="select select-ghost"
+                    value={v.map?.[binding]?.column}
+                    ref={(el) => {
+                      columnsRef.current[binding] = el;
+                    }}
+                    onChange={() => onChange(JSON.stringify({ map: getMap() }))}
+                  >
+                    <option key="" value="" />
+                    {dfs[v.map?.[binding]?.df]?.map((col: string) => (
+                      <option key={col} value={col}>
+                        {col}
+                      </option>
+                    ))}
+                  </select>
+                )}
+              </td>
+            </tr>
+          ))
+        ) : (
+          <tr>
+            <td>no bindings</td>
+          </tr>
+        )}
+      </tbody>
+    </table>
   );
 }
 
@@ -10,15 +188,11 @@ interface NodeParameterProps {
   name: string;
   value: any;
   meta: any;
+  data: any;
   onChange: (value: any, options?: { delay: number }) => void;
 }
 
-export default function NodeParameter({
-  name,
-  value,
-  meta,
-  onChange,
-}: NodeParameterProps) {
+export default function NodeParameter({ name, value, meta, data, onChange }: NodeParameterProps) {
   return (
     // biome-ignore lint/a11y/noLabelWithoutControl: Most of the time there is a control.
     <label className="param">
@@ -56,28 +230,34 @@ export default function NodeParameter({
       ) : meta?.type?.type === BOOLEAN ? (
         <div className="form-control">
           <label className="label cursor-pointer">
+            {name.replace(/_/g, " ")}
             <input
               className="checkbox"
               type="checkbox"
               checked={value}
               onChange={(evt) => onChange(evt.currentTarget.checked)}
             />
-            {name.replace(/_/g, " ")}
           </label>
         </div>
+      ) : meta?.type?.type === MODEL_TRAINING_INPUT_MAPPING ? (
+        <>
+          <ParamName name={name} />
+          <ModelMapping value={value} data={data} variant="training input" onChange={onChange} />
+        </>
+      ) : meta?.type?.type === MODEL_INFERENCE_INPUT_MAPPING ? (
+        <>
+          <ParamName name={name} />
+          <ModelMapping value={value} data={data} variant="inference input" onChange={onChange} />
+        </>
+      ) : meta?.type?.type === MODEL_OUTPUT_MAPPING ? (
+        <>
+          <ParamName name={name} />
+          <ModelMapping value={value} data={data} variant="output" onChange={onChange} />
+        </>
       ) : (
         <>
           <ParamName name={name} />
-          <input
-            className="input input-bordered w-full"
-            value={value || ""}
-            onChange={(evt) => onChange(evt.currentTarget.value, { delay: 2 })}
-            onBlur={(evt) => onChange(evt.currentTarget.value, { delay: 0 })}
-            onKeyDown={(evt) =>
-              evt.code === "Enter" &&
-              onChange(evt.currentTarget.value, { delay: 0 })
-            }
-          />
+          <Input value={value} onChange={onChange} />
         </>
       )}
     </label>

lynxkite-app/web/src/workspace/nodes/NodeWithImage.tsx

@@ -3,9 +3,7 @@ import NodeWithParams from "./NodeWithParams";
 const NodeWithImage = (props: any) => {
   return (
     <NodeWithParams {...props}>
-      {props.data.display && (
-        <img src={props.data.display} alt="Node Display" />
-      )}
+      {props.data.display && <img src={props.data.display} alt="Node Display" />}
     </NodeWithParams>
   );
 };

lynxkite-app/web/src/workspace/nodes/NodeWithParams.tsx

@@ -35,11 +35,8 @@ function NodeWithParams(props: any) {
 
   return (
     <LynxKiteNode {...props}>
-      {props.collapsed && (
-        <div
-          className="params-expander"
-          onClick={() => setCollapsed(!collapsed)}
-        >
+      {props.collapsed && params.length > 0 && (
+        <div className="params-expander" onClick={() => setCollapsed(!collapsed)}>
           <Triangle className={`flippy ${collapsed ? "flippy-90" : ""}`} />
         </div>
       )}
@@ -49,23 +46,21 @@ function NodeWithParams(props: any) {
             <NodeGroupParameter
               key={name}
               value={value}
+              data={props.data}
               meta={metaParams?.[name]}
               setParam={(name: string, value: any, opts?: UpdateOptions) =>
                 setParam(name, value, opts || {})
               }
-              deleteParam={(name: string, opts?: UpdateOptions) =>
-                deleteParam(name, opts || {})
-              }
+              deleteParam={(name: string, opts?: UpdateOptions) => deleteParam(name, opts || {})}
             />
           ) : (
             <NodeParameter
               name={name}
               key={name}
               value={value}
+              data={props.data}
               meta={metaParams?.[name]}
-              onChange={(value: any, opts?: UpdateOptions) =>
-                setParam(name, value, opts || {})
-              }
+              onChange={(value: any, opts?: UpdateOptions) => setParam(name, value, opts || {})}
             />
           ),
         )}

lynxkite-app/web/src/workspace/nodes/NodeWithTableView.tsx

@@ -1,3 +1,4 @@
+import { useReactFlow } from "@xyflow/react";
 import { useState } from "react";
 import React from "react";
 import Markdown from "react-markdown";
@@ -14,34 +15,41 @@ function toMD(v: any): string {
   return JSON.stringify(v);
 }
 
+type OpenState = { [name: string]: boolean };
+
 export default function NodeWithTableView(props: any) {
-  const [open, setOpen] = useState({} as { [name: string]: boolean });
+  const reactFlow = useReactFlow();
+  const [open, setOpen] = useState((props.data?.params?._tables_open ?? {}) as OpenState);
   const display = props.data.display?.value;
-  const single =
-    display?.dataframes && Object.keys(display?.dataframes).length === 1;
+  const single = display?.dataframes && Object.keys(display?.dataframes).length === 1;
   const dfs = Object.entries(display?.dataframes || {});
   dfs.sort();
+  function setParam(name: string, newValue: any) {
+    reactFlow.updateNodeData(props.id, (prevData: any) => ({
+      ...prevData,
+      params: { ...prevData.data.params, [name]: newValue },
+    }));
+  }
+  function toggleTable(name: string) {
+    setOpen((prevOpen: OpenState) => {
+      const newOpen = { ...prevOpen, [name]: !prevOpen[name] };
+      setParam("_tables_open", newOpen);
+      return newOpen;
+    });
+  }
   return (
     <LynxKiteNode {...props}>
       {display && [
         dfs.map(([name, df]: [string, any]) => (
           <React.Fragment key={name}>
             {!single && (
-              <div
-                key={`${name}-header`}
-                className="df-head"
-                onClick={() => setOpen({ ...open, [name]: !open[name] })}
-              >
+              <div key={`${name}-header`} className="df-head" onClick={() => toggleTable(name)}>
                 {name}
               </div>
             )}
             {(single || open[name]) &&
               (df.data.length > 1 ? (
-                <Table
-                  key={`${name}-table`}
-                  columns={df.columns}
-                  data={df.data}
-                />
+                <Table key={`${name}-table`} columns={df.columns} data={df.data} />
               ) : df.data.length ? (
                 <dl key={`${name}-dl`}>
                   {df.columns.map((c: string, i: number) => (
@@ -60,11 +68,7 @@ export default function NodeWithTableView(props: any) {
         )),
         Object.entries(display.others || {}).map(([name, o]) => (
           <>
-            <div
-              key={`${name}-header`}
-              className="df-head"
-              onClick={() => setOpen({ ...open, [name]: !open[name] })}
-            >
+            <div key={`${name}-header`} className="df-head" onClick={() => toggleTable(name)}>
               {name}
             </div>
             {open[name] && <pre>{(o as any).toString()}</pre>}

lynxkite-app/web/src/workspace/nodes/NodeWithVisualization.tsx

@@ -8,6 +8,10 @@ const NodeWithVisualization = (props: any) => {
   useEffect(() => {
     const opts = props.data?.display?.value;
     if (!opts || !chartsRef.current) return;
+    if (opts.tooltip?.formatter === "GET_THIRD_VALUE") {
+      // We can't pass a function from the backend, and can't get good tooltips otherwise.
+      opts.tooltip.formatter = (params: any) => params.value[2];
+    }
     chartsInstanceRef.current = echarts.init(chartsRef.current, null, {
       renderer: "canvas",
       width: "auto",

lynxkite-app/web/tests/directory.spec.ts

@@ -14,13 +14,6 @@ test.describe("Directory operations", () => {
     splash = await Splash.open(page);
   });
 
-  test("Create workspace with default name", async () => {
-    const workspace = await Workspace.empty(splash.page);
-    // Not checking for exact match, since there may be pre-existing "Untitled" workspaces
-    expect(workspace.name).toContain("Untitled");
-    await workspace.close();
-  });
-
   test("Create & delete workspace", async () => {
     const workspaceName = `TestWorkspace-${Date.now()}`;
     const workspace = await Workspace.empty(splash.page, workspaceName);
@@ -40,11 +33,6 @@ test.describe("Directory operations", () => {
     await splash.deleteEntry(folderName);
     await expect(splash.getEntry(folderName)).not.toBeVisible();
   });
-
-  test("Create folder with default name", async () => {
-    await splash.createFolder();
-    await expect(splash.currentFolder()).toContainText("Untitled");
-  });
 });
 
 test.describe

lynxkite-app/web/tests/errors.spec.ts

@@ -35,9 +35,7 @@ test("unknown operation", async () => {
   await graphBox.getByLabel("n", { exact: true }).fill("10");
   await workspace.setEnv("LynxScribe");
   const csvBox = workspace.getBox("NX › Scale-Free Graph 1");
-  await expect(csvBox.locator(".error")).toHaveText(
-    'Operation "NX › Scale-Free Graph" not found.',
-  );
+  await expect(csvBox.locator(".error")).toHaveText('Operation "NX › Scale-Free Graph" not found.');
   await workspace.setEnv("LynxKite Graph Analytics");
   await expect(csvBox.locator(".error")).not.toBeVisible();
 });

lynxkite-app/web/tests/graph_creation.spec.ts

@@ -5,15 +5,9 @@ import { Splash, Workspace } from "./lynxkite";
 let workspace: Workspace;
 
 test.beforeEach(async ({ browser }) => {
-  workspace = await Workspace.empty(
-    await browser.newPage(),
-    "graph_creation_spec_test",
-  );
+  workspace = await Workspace.empty(await browser.newPage(), "graph_creation_spec_test");
   await workspace.addBox("NX › Scale-Free Graph");
-  await workspace
-    .getBox("NX › Scale-Free Graph 1")
-    .getByLabel("n", { exact: true })
-    .fill("10");
+  await workspace.getBox("NX › Scale-Free Graph 1").getByLabel("n", { exact: true }).fill("10");
   await workspace.addBox("Create graph");
   await workspace.connectBoxes("NX › Scale-Free Graph 1", "Create graph 1");
 });
@@ -45,9 +39,7 @@ test("Tables are displayed in the Graph creation box", async () => {
 
 test("Adding and removing relationships", async () => {
   const graphBox = await workspace.getBox("Create graph 1");
-  const addRelationshipButton = await graphBox.locator(
-    ".add-relationship-button",
-  );
+  const addRelationshipButton = await graphBox.locator(".add-relationship-button");
   await addRelationshipButton.click();
   const formData: Record<string, string> = {
     name: "relation_1",
@@ -69,10 +61,9 @@ test("Adding and removing relationships", async () => {
   // check that the relationship has been saved in the backend
   await workspace.page.reload();
   const graphBoxAfterReload = await workspace.getBox("Create graph 1");
-  const relationHeader = await graphBoxAfterReload.locator(
-    ".graph-relations .df-head",
-    { hasText: "relation_1" },
-  );
+  const relationHeader = await graphBoxAfterReload.locator(".graph-relations .df-head", {
+    hasText: "relation_1",
+  });
   await expect(relationHeader).toBeVisible();
   await relationHeader.locator("button").click(); // Delete the relationship
   await expect(relationHeader).not.toBeVisible();