PytorchConnectomics · zhangdjr · Apr 3, 2026
diff --git a/.logs/start/api-server.log b/.logs/start/api-server.log
@@ -0,0 +1,35 @@
+INFO:     Started server process [69167]
+INFO:     Waiting for application startup.
+INFO:     Application startup complete.
+INFO:     Uvicorn running on http://0.0.0.0:4242 (Press CTRL+C to quit)
+================================================================================
+EHTOOL ROUTER MODULE LOADED - VERSION: DEBUG v2
+================================================================================
+INFO:     127.0.0.1:60334 - "GET /health HTTP/1.1" 200 OK
+INFO:     127.0.0.1:60379 - "GET /files?parent=root HTTP/1.1" 200 OK
+INFO:     127.0.0.1:60383 - "GET /chat/conversations HTTP/1.1" 200 OK
+INFO:     127.0.0.1:60383 - "GET /chat/conversations HTTP/1.1" 200 OK
+INFO:     127.0.0.1:60383 - "OPTIONS /chat/conversations/1 HTTP/1.1" 200 OK
+INFO:     127.0.0.1:60383 - "DELETE /chat/conversations/1 HTTP/1.1" 200 OK
+INFO:     127.0.0.1:60389 - "OPTIONS /chat/query HTTP/1.1" 200 OK
+[SEARCH] Loaded 7 docs for keyword search: ['MaskProofreading.md', 'FileManager.md', 'ModelInference.md', 'GettingStarted.md', 'ModelTraining.md', 'Visualization.md', 'Monitoring.md']
+[TOOL] search_documentation(query='upload training data server PyTC Client upload training data to server') [call 1]
+[TOOL] RAG → 2 chunks: ['GettingStarted.md', 'ModelTraining.md']
+[TOOL] search_documentation(query='File Manager upload training data PyTC Client') [call 2]
+[TOOL] RAG → 2 chunks: ['FileManager.md', 'ModelTraining.md']
+INFO:     127.0.0.1:60389 - "POST /chat/query HTTP/1.1" 200 OK
+INFO:     127.0.0.1:60389 - "GET /chat/conversations HTTP/1.1" 200 OK
+[TOOL] search_documentation(query='training workflow what do I need to provide PyTC Client training new model') [call 1]
+[TOOL] RAG → 2 chunks: ['GettingStarted.md', 'ModelInference.md']
+[TOOL] search_documentation(query='Model Training page what inputs are required PyTC Client') [call 2]
+[TOOL] RAG → 2 chunks: ['GettingStarted.md', 'ModelTraining.md']
+INFO:     127.0.0.1:60389 - "POST /chat/query HTTP/1.1" 200 OK
+INFO:     127.0.0.1:60389 - "GET /chat/conversations HTTP/1.1" 200 OK
+[TOOL] search_documentation(query='monitor training progress real-time PyTC Client UI') [call 1]
+[TOOL] RAG → 2 chunks: ['ModelTraining.md', 'GettingStarted.md']
+INFO:     127.0.0.1:60502 - "POST /chat/query HTTP/1.1" 200 OK
+INFO:     127.0.0.1:60502 - "GET /chat/conversations HTTP/1.1" 200 OK
+INFO:     Shutting down
+INFO:     Waiting for application shutdown.
+INFO:     Application shutdown complete.
+INFO:     Finished server process [69167]
diff --git a/.logs/start/data-server.log b/.logs/start/data-server.log
@@ -0,0 +1 @@
+127.0.0.1 - - [03/Apr/2026 15:13:18] "GET / HTTP/1.1" 200 -
diff --git a/.logs/start/pytc-server.log b/.logs/start/pytc-server.log
@@ -0,0 +1,21 @@
+INFO:     Started server process [69189]
+INFO:     Waiting for application startup.
+INFO:     Application startup complete.
+INFO:     Uvicorn running on http://0.0.0.0:4243 (Press CTRL+C to quit)
+
+================================================================================
+SERVER_PYTC STARTING UP
+Python executable: /Users/tizhang/Desktop/pytc-client/.venv/bin/python3
+Working directory: /Users/tizhang/Desktop/pytc-client
+================================================================================
+
+
+================================================================================
+SERVER_PYTC: Starting Uvicorn server on port 4243...
+================================================================================
+
+INFO:     127.0.0.1:60339 - "GET /hello HTTP/1.1" 200 OK
+INFO:     Shutting down
+INFO:     Waiting for application shutdown.
+INFO:     Application shutdown complete.
+INFO:     Finished server process [69189]
diff --git a/.logs/start/react-build.log b/.logs/start/react-build.log
@@ -0,0 +1,67 @@
+npm warn Unknown user config "always-auth". This will stop working in the next major version of npm.
+npm warn Unknown user config "always-auth" (//firelayers.jfrog.io/artifactory/api/npm/itc-npm-virtual/:always-auth). This will stop working in the next major version of npm.
+
+> PyTC Client@0.1.0 build
+> cross-env CI=false react-scripts build
+
+[baseline-browser-mapping] The data in this module is over two months old.  To ensure accurate Baseline data, please update: `npm i baseline-browser-mapping@latest -D`
+Creating an optimized production build...
+[baseline-browser-mapping] The data in this module is over two months old.  To ensure accurate Baseline data, please update: `npm i baseline-browser-mapping@latest -D`
+Compiled with warnings.
+
+[eslint] 
+src/components/FilePickerModal.js
+  Line 102:35:  Function declared in a loop contains unsafe references to variable(s) 'curr'                                                                                                                                                                                                                                                                                              no-loop-func
+  Line 124:35:  Function declared in a loop contains unsafe references to variable(s) 'currParentId'                                                                                                                                                                                                                                                                                      no-loop-func
+  Line 243:15:  The href attribute is required for an anchor to be keyboard accessible. Provide a valid, navigable address as the href value. If you cannot provide an href, but still need the element to resemble a link, use a button and change it with appropriate styles. Learn more: https://github.com/jsx-eslint/eslint-plugin-jsx-a11y/blob/HEAD/docs/rules/anchor-is-valid.md  jsx-a11y/anchor-is-valid
+
+src/components/YamlFileUploader.js
+  Line 347:6:  React Hook useEffect has missing dependencies: 'getCurrentConfig' and 'syncYamlContext'. Either include them or remove the dependency array                                      react-hooks/exhaustive-deps
+  Line 361:6:  React Hook useEffect has missing dependencies: 'getCurrentConfig', 'setCurrentConfig', and 'updateInputSelectorInformation'. Either include them or remove the dependency array  react-hooks/exhaustive-deps
+  Line 374:6:  React Hook useMemo has a missing dependency: 'getCurrentConfig'. Either include it or remove the dependency array                                                                react-hooks/exhaustive-deps
+
+src/views/EHTool.js
+  Line 25:6:  React Hook useEffect has a missing dependency: 'sessionId'. Either include it or remove the dependency array  react-hooks/exhaustive-deps
+
+src/views/FilesManager.js
+  Line 81:31:   Function declared in a loop contains unsafe references to variable(s) 'current'                                                                                                                        no-loop-func
+  Line 424:27:  Function declared in a loop contains unsafe references to variable(s) 'curr'                                                                                                                           no-loop-func
+  Line 776:32:  Function declared in a loop contains unsafe references to variable(s) 'descendantSizeKb', 'descendantSizeKb', 'descendantSizeKb', 'descendantSizeKb'                                                   no-loop-func
+  Line 1073:6:  React Hook useEffect has missing dependencies: 'finishCreateFolder', 'finishRename', 'handleCopy', 'handleCut', 'handleDelete', and 'handlePaste'. Either include them or remove the dependency array  react-hooks/exhaustive-deps
+
+src/views/ehtool/DetectionWorkflow.js
+  Line 225:6:   React Hook useEffect has a missing dependency: 'loadInstances'. Either include it or remove the dependency array                                                                                                                                                         react-hooks/exhaustive-deps
+  Line 274:20:  The ref value 'schedulerRef.current' will likely have changed by the time this effect cleanup function runs. If this ref points to a node rendered by React, copy 'schedulerRef.current' to a variable inside the effect, and use that variable in the cleanup function  react-hooks/exhaustive-deps
+  Line 314:6:   React Hook useEffect has a missing dependency: 'loadInstanceView'. Either include it or remove the dependency array                                                                                                                                                      react-hooks/exhaustive-deps
+  Line 355:6:   React Hook useEffect has a missing dependency: 'loadInstanceView'. Either include it or remove the dependency array                                                                                                                                                      react-hooks/exhaustive-deps
+  Line 416:6:   React Hook useEffect has missing dependencies: 'goToNextInstance', 'goToPreviousInstance', 'handleAxisChange', and 'handleInstanceClassify'. Either include them or remove the dependency array                                                                          react-hooks/exhaustive-deps
+  Line 524:6:   React Hook useEffect has a missing dependency: 'clearFrameCaches'. Either include it or remove the dependency array                                                                                                                                                      react-hooks/exhaustive-deps
+
+src/views/ehtool/ProofreadingEditor.js
+  Line 140:8:  React Hook useEffect has a missing dependency: 'loadImages'. Either include it or remove the dependency array                                    react-hooks/exhaustive-deps
+  Line 148:8:  React Hook useEffect has missing dependencies: 'drawCanvas' and 'drawMinimap'. Either include them or remove the dependency array                react-hooks/exhaustive-deps
+  Line 163:8:  React Hook useEffect has missing dependencies: 'drawCanvas' and 'drawMinimap'. Either include them or remove the dependency array                react-hooks/exhaustive-deps
+  Line 403:8:  React Hook useEffect has a missing dependency: 'loadOverlayImage'. Either include it or remove the dependency array                              react-hooks/exhaustive-deps
+  Line 407:8:  React Hook useEffect has a missing dependency: 'loadOverlayImage'. Either include it or remove the dependency array                              react-hooks/exhaustive-deps
+  Line 653:7:  React Hook useMemo has a missing dependency: 'glasbeyColor'. Either include it or remove the dependency array                                    react-hooks/exhaustive-deps
+  Line 662:8:  React Hook useEffect has missing dependencies: 'drawCanvas' and 'drawMinimap'. Either include them or remove the dependency array                react-hooks/exhaustive-deps
+  Line 899:9:  Expected a default case                                                                                                                          default-case
+  Line 940:8:  React Hook useEffect has missing dependencies: 'handleRedo', 'handleSave', and 'handleUndo'. Either include them or remove the dependency array  react-hooks/exhaustive-deps
+
+Search for the keywords to learn more about each warning.
+To ignore, add // eslint-disable-next-line to the line before.
+
+File sizes after gzip:
+
+  481.63 kB  build/static/js/main.ea9ff1f9.js
+  465 B      build/static/css/main.40821645.css
+
+The project was built assuming it is hosted at ./.
+You can control this with the homepage field in your package.json.
+
+The build folder is ready to be deployed.
+
+Find out more about deployment here:
+
+  https://cra.link/deployment
+
diff --git a/.logs/start/react-dev.log b/.logs/start/react-dev.log
@@ -0,0 +1,23 @@
+npm warn Unknown user config "always-auth". This will stop working in the next major version of npm.
+npm warn Unknown user config "always-auth" (//firelayers.jfrog.io/artifactory/api/npm/itc-npm-virtual/:always-auth). This will stop working in the next major version of npm.
+
+> PyTC Client@0.1.0 start
+> react-scripts start
+
+[baseline-browser-mapping] The data in this module is over two months old.  To ensure accurate Baseline data, please update: `npm i baseline-browser-mapping@latest -D`
+(node:69273) [DEP_WEBPACK_DEV_SERVER_ON_AFTER_SETUP_MIDDLEWARE] DeprecationWarning: 'onAfterSetupMiddleware' option is deprecated. Please use the 'setupMiddlewares' option.
+(Use `node --trace-deprecation ...` to show where the warning was created)
+(node:69273) [DEP_WEBPACK_DEV_SERVER_ON_BEFORE_SETUP_MIDDLEWARE] DeprecationWarning: 'onBeforeSetupMiddleware' option is deprecated. Please use the 'setupMiddlewares' option.
+Starting the development server...
+
+Compiled successfully!
+
+You can now view PyTC Client in the browser.
+
+  Local:            http://localhost:3000
+  On Your Network:  http://192.168.99.154:3000
+
+Note that the development build is not optimized.
+To create a production build, use npm run build.
+
+webpack compiled successfully
diff --git a/client/preload.js b/client/preload.js
@@ -2,7 +2,8 @@ const { contextBridge, ipcRenderer } = require("electron");
 
 contextBridge.exposeInMainWorld("electronAPI", {
   isElectron: true,
-  openLocalFile: (options = {}) => ipcRenderer.invoke("open-local-file", options),
+  openLocalFile: (options = {}) =>
+    ipcRenderer.invoke("open-local-file", options),
   revealInFinder: (targetPath) =>
     ipcRenderer.invoke("reveal-in-finder", targetPath),
 });
diff --git a/client/src/components/RuntimeLogPanel.js b/client/src/components/RuntimeLogPanel.js
@@ -117,7 +117,7 @@ function RuntimeLogPanel({ title, runtime, onRefresh }) {
               background: "#fff",
               border: "1px solid #f0f0f0",
               fontFamily:
-                'ui-monospace, SFMono-Regular, SF Mono, Menlo, Consolas, monospace',
+                "ui-monospace, SFMono-Regular, SF Mono, Menlo, Consolas, monospace",
               fontSize: 12,
               color: "#262626",
               wordBreak: "break-word",
@@ -142,7 +142,7 @@ function RuntimeLogPanel({ title, runtime, onRefresh }) {
             whiteSpace: "pre-wrap",
             wordBreak: "break-word",
             fontFamily:
-              'ui-monospace, SFMono-Regular, SF Mono, Menlo, Consolas, monospace',
+              "ui-monospace, SFMono-Regular, SF Mono, Menlo, Consolas, monospace",
           }}
         >
           {text || "No runtime logs captured yet."}

diff --git a/client/src/components/YamlFileUploader.js b/client/src/components/YamlFileUploader.js
@@ -490,7 +490,11 @@ const YamlFileUploader = (props) => {
       {yamlContent ? (
         <Row>
           {sliderData.map((param, index) => {
-            const sliderValue = getSliderValue(currentYamlData, type, param.key);
+            const sliderValue = getSliderValue(
+              currentYamlData,
+              type,
+              param.key,
+            );
             const sliderSupported = isSliderSupported(
               currentYamlData,
               type,
@@ -507,7 +511,11 @@ const YamlFileUploader = (props) => {
                       min={param.min}
                       max={param.max}
                       marks={param.marks}
-                      value={typeof sliderValue === "number" ? sliderValue : param.value}
+                      value={
+                        typeof sliderValue === "number"
+                          ? sliderValue
+                          : param.value
+                      }
                       disabled={!sliderSupported}
                       onChange={(newValue) =>
                         handleSliderChange(param.key, newValue)

diff --git a/client/src/configSchema.js b/client/src/configSchema.js
@@ -135,14 +135,26 @@ export function setTrainingOutputPath(configObj, outputPath) {
   }
   const checkpointsPath = joinPath(outputPath, "checkpoints");
   if (hasPath(configObj, ["train", "monitor", "checkpoint", "dirpath"])) {
-    setPathValue(configObj, ["train", "monitor", "checkpoint", "dirpath"], checkpointsPath);
+    setPathValue(
+      configObj,
+      ["train", "monitor", "checkpoint", "dirpath"],
+      checkpointsPath,
+    );
     return;
   }
   if (hasPath(configObj, ["monitor", "checkpoint", "dirpath"])) {
-    setPathValue(configObj, ["monitor", "checkpoint", "dirpath"], checkpointsPath);
+    setPathValue(
+      configObj,
+      ["monitor", "checkpoint", "dirpath"],
+      checkpointsPath,
+    );
     return;
   }
-  setPathValue(configObj, ["monitor", "checkpoint", "dirpath"], checkpointsPath);
+  setPathValue(
+    configObj,
+    ["monitor", "checkpoint", "dirpath"],
+    checkpointsPath,
+  );
 }
 
 export function setInferenceOutputPath(configObj, outputPath) {
@@ -152,7 +164,11 @@ export function setInferenceOutputPath(configObj, outputPath) {
     setPathValue(configObj, ["INFERENCE", "OUTPUT_PATH"], outputPath);
     return;
   }
-  setPathValue(configObj, ["inference", "save_prediction", "output_path"], outputPath);
+  setPathValue(
+    configObj,
+    ["inference", "save_prediction", "output_path"],
+    outputPath,
+  );
 }
 
 export function setInferenceExecutionDefaults(configObj) {
@@ -212,16 +228,14 @@ export function applyInputPaths(
   }
 
   if (mode === "training") {
-    const imagePath =
-      pickFirstExistingPath(configObj, [
-        ["train", "data", "train", "image"],
-        ["data", "train", "image"],
-      ]) || ["train", "data", "train", "image"];
-    const labelPath =
-      pickFirstExistingPath(configObj, [
-        ["train", "data", "train", "label"],
-        ["data", "train", "label"],
-      ]) || ["train", "data", "train", "label"];
+    const imagePath = pickFirstExistingPath(configObj, [
+      ["train", "data", "train", "image"],
+      ["data", "train", "image"],
+    ]) || ["train", "data", "train", "image"];
+    const labelPath = pickFirstExistingPath(configObj, [
+      ["train", "data", "train", "label"],
+      ["data", "train", "label"],
+    ]) || ["train", "data", "train", "label"];
     setPathValue(configObj, imagePath, inputImagePath);
     setPathValue(configObj, labelPath, inputLabelPath);
     if (outputPath) {
@@ -230,16 +244,14 @@ export function applyInputPaths(
     return;
   }
 
-  const imagePath =
-    pickFirstExistingPath(configObj, [
-      ["test", "data", "test", "image"],
-      ["data", "test", "image"],
-    ]) || ["test", "data", "test", "image"];
-  const labelPath =
-    pickFirstExistingPath(configObj, [
-      ["test", "data", "test", "label"],
-      ["data", "test", "label"],
-    ]) || ["test", "data", "test", "label"];
+  const imagePath = pickFirstExistingPath(configObj, [
+    ["test", "data", "test", "image"],
+    ["data", "test", "image"],
+  ]) || ["test", "data", "test", "image"];
+  const labelPath = pickFirstExistingPath(configObj, [
+    ["test", "data", "test", "label"],
+    ["data", "test", "label"],
+  ]) || ["test", "data", "test", "label"];
   setPathValue(configObj, imagePath, inputImagePath);
   if (hasLabelPath) {
     setPathValue(configObj, labelPath, inputLabelPath);

diff --git a/client/src/configSchema.test.js b/client/src/configSchema.test.js
@@ -1,7 +1,4 @@
-import {
-  applyInputPaths,
-  setInferenceExecutionDefaults,
-} from "./configSchema";
+import { applyInputPaths, setInferenceExecutionDefaults } from "./configSchema";
 
 describe("setInferenceExecutionDefaults", () => {
   it("preserves existing legacy GPU values", () => {

diff --git a/client/src/contexts/GlobalContext.js b/client/src/contexts/GlobalContext.js
@@ -130,25 +130,13 @@ export const ContextWrapper = (props) => {
   const [inferenceConfigOriginPath, setInferenceConfigOriginPath] =
     usePersistedState("inferenceConfigOriginPath", "");
   const [trainingUploadedYamlFile, setTrainingUploadedYamlFile] =
-    usePersistedState(
-      "trainingUploadedYamlFile",
-      "",
-    );
+    usePersistedState("trainingUploadedYamlFile", "");
   const [inferenceUploadedYamlFile, setInferenceUploadedYamlFile] =
-    usePersistedState(
-      "inferenceUploadedYamlFile",
-      "",
-    );
+    usePersistedState("inferenceUploadedYamlFile", "");
   const [trainingSelectedYamlPreset, setTrainingSelectedYamlPreset] =
-    usePersistedState(
-      "trainingSelectedYamlPreset",
-      "",
-    );
+    usePersistedState("trainingSelectedYamlPreset", "");
   const [inferenceSelectedYamlPreset, setInferenceSelectedYamlPreset] =
-    usePersistedState(
-      "inferenceSelectedYamlPreset",
-      "",
-    );
+    usePersistedState("inferenceSelectedYamlPreset", "");
   const [imageFileList, setImageFileList] = usePersistedState(
     "imageFileList",
     [],
@@ -170,10 +158,7 @@ export const ContextWrapper = (props) => {
     null,
   );
   const [inferenceCheckpointPath, setInferenceCheckpointPath] =
-    usePersistedState(
-      "inferenceCheckpointPath",
-      null,
-    );
+    usePersistedState("inferenceCheckpointPath", null);
   const [currentImage, setCurrentImage] = usePersistedState(
     "currentImage",
     null,
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		127.0.0.1 - - [03/Apr/2026 15:13:18] "GET / HTTP/1.1" 200 -