Merge main into docker

.devcontainer/dev-amd-wsl/devcontainer.json

@@ -0,0 +1,75 @@
+{
+  "name": "OncoLearn (AMD-WSL)",
+  "dockerComposeFile": "../../docker-compose.yml",
+  "service": "dev-amd-wsl",
+  "runServices": ["dev-amd-wsl"],
+  "workspaceFolder": "/workspace",
+
+  // Configure which extensions should be installed
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "charliermarsh.ruff",
+        "ms-python.autopep8",
+        "REditorSupport.r",
+        "ms-toolsai.jupyter",
+        "ms-toolsai.vscode-jupyter-cell-tags",
+        "ms-toolsai.vscode-jupyter-slideshow",
+        "ms-azuretools.vscode-docker",
+        "tamasfe.even-better-toml"
+      ],
+      "settings": {
+        "python.defaultInterpreterPath": "/workspace/.venv/bin/python",
+        "python.terminal.activateEnvironment": true,
+        "python.analysis.autoFormatStrings": true,
+        "jupyter.notebookFileRoot": "${workspaceFolder}",
+        "terminal.integrated.defaultProfile.linux": "bash",
+        "autopep8.path": ["/workspace/.venv/bin/autopep8"],
+        "ruff.path": ["/workspace/.venv/bin/ruff"],
+        "ruff.interpreter": ["/workspace/.venv/bin/python"],
+        "[python]": {
+          "editor.tabSize": 4,
+          "editor.insertSpaces": true,
+          "editor.rulers": [120],
+          "editor.defaultFormatter": "ms-python.autopep8",
+          "editor.formatOnSave": true,
+          "editor.codeActionsOnSave": {
+            "source.fixAll": "explicit",
+            "source.organizeImports": "explicit"
+          }
+        },
+        "notebook.formatOnSave.enabled": true,
+        "notebook.codeActionsOnSave": {
+          "notebook.source.fixAll": "explicit",
+          "notebook.source.organizeImports": "explicit"
+        }
+      }
+    }
+  },
+
+  // Expose Jupyter port
+  "forwardPorts": [8888],
+  "portsAttributes": {
+    "8888": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Keep container running
+  "shutdownAction": "stopCompose",
+
+  // Run as root (can be changed for better security)
+  "remoteUser": "root",
+
+  // Run uv sync on container start
+  "postStartCommand": "uv sync --extra rocm",
+
+  // Features to add
+  "features": {
+    "ghcr.io/devcontainers/features/git:1": {},
+    "ghcr.io/devcontainers/features/github-cli:1": {}
+  }
+}

.devcontainer/dev-amd/devcontainer.json

@@ -0,0 +1,75 @@
+{
+  "name": "OncoLearn (AMD)",
+  "dockerComposeFile": "../../docker-compose.yml",
+  "service": "dev-amd",
+  "runServices": ["dev-amd"],
+  "workspaceFolder": "/workspace",
+
+  // Configure which extensions should be installed
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "charliermarsh.ruff",
+        "ms-python.autopep8",
+        "REditorSupport.r",
+        "ms-toolsai.jupyter",
+        "ms-toolsai.vscode-jupyter-cell-tags",
+        "ms-toolsai.vscode-jupyter-slideshow",
+        "ms-azuretools.vscode-docker",
+        "tamasfe.even-better-toml"
+      ],
+      "settings": {
+        "python.defaultInterpreterPath": "/workspace/.venv/bin/python",
+        "python.terminal.activateEnvironment": true,
+        "python.analysis.autoFormatStrings": true,
+        "jupyter.notebookFileRoot": "${workspaceFolder}",
+        "terminal.integrated.defaultProfile.linux": "bash",
+        "autopep8.path": ["/workspace/.venv/bin/autopep8"],
+        "ruff.path": ["/workspace/.venv/bin/ruff"],
+        "ruff.interpreter": ["/workspace/.venv/bin/python"],
+        "[python]": {
+          "editor.tabSize": 4,
+          "editor.insertSpaces": true,
+          "editor.rulers": [120],
+          "editor.defaultFormatter": "ms-python.autopep8",
+          "editor.formatOnSave": true,
+          "editor.codeActionsOnSave": {
+            "source.fixAll": "explicit",
+            "source.organizeImports": "explicit"
+          }
+        },
+        "notebook.formatOnSave.enabled": true,
+        "notebook.codeActionsOnSave": {
+          "notebook.source.fixAll": "explicit",
+          "notebook.source.organizeImports": "explicit"
+        }
+      }
+    }
+  },
+
+  // Expose Jupyter port
+  "forwardPorts": [8888],
+  "portsAttributes": {
+    "8888": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Keep container running
+  "shutdownAction": "stopCompose",
+
+  // Run as root (can be changed for better security)
+  "remoteUser": "root",
+
+  // Run uv sync on container start
+  "postStartCommand": "uv sync --extra rocm",
+
+  // Features to add
+  "features": {
+    "ghcr.io/devcontainers/features/git:1": {},
+    "ghcr.io/devcontainers/features/github-cli:1": {}
+  }
+}

.devcontainer/devcontainer.json → .devcontainer/dev-cpu/devcontainer.json

@@ -1,7 +1,8 @@
 {
-  "name": "OncoLearn",
-  "dockerComposeFile": "../docker-compose.yml",
-  "service": "dev",
+  "name": "OncoLearn (CPU)",
+  "dockerComposeFile": "../../docker-compose.yml",
+  "service": "dev-cpu",
+  "runServices": ["dev-cpu"],
   "workspaceFolder": "/workspace",
 
   // Configure which extensions should be installed
@@ -16,16 +17,34 @@
         "ms-toolsai.jupyter",
         "ms-toolsai.vscode-jupyter-cell-tags",
         "ms-toolsai.vscode-jupyter-slideshow",
-        "ms-azuretools.vscode-docker"
+        "ms-azuretools.vscode-docker",
+        "tamasfe.even-better-toml"
       ],
       "settings": {
         "python.defaultInterpreterPath": "/workspace/.venv/bin/python",
         "python.terminal.activateEnvironment": true,
+        "python.analysis.autoFormatStrings": true,
         "jupyter.notebookFileRoot": "${workspaceFolder}",
         "terminal.integrated.defaultProfile.linux": "bash",
         "autopep8.path": ["/workspace/.venv/bin/autopep8"],
         "ruff.path": ["/workspace/.venv/bin/ruff"],
-        "ruff.interpreter": ["/workspace/.venv/bin/python"]
+        "ruff.interpreter": ["/workspace/.venv/bin/python"],
+        "[python]": {
+          "editor.tabSize": 4,
+          "editor.insertSpaces": true,
+          "editor.rulers": [120],
+          "editor.defaultFormatter": "ms-python.autopep8",
+          "editor.formatOnSave": true,
+          "editor.codeActionsOnSave": {
+            "source.fixAll": "explicit",
+            "source.organizeImports": "explicit"
+          }
+        },
+        "notebook.formatOnSave.enabled": true,
+        "notebook.codeActionsOnSave": {
+          "notebook.source.fixAll": "explicit",
+          "notebook.source.organizeImports": "explicit"
+        }
       }
     }
   },
@@ -39,15 +58,15 @@
     }
   },
 
-  // Post-create command
-  "postCreateCommand": "uv sync --extra cu130",
-
   // Keep container running
   "shutdownAction": "stopCompose",
 
   // Run as root (can be changed for better security)
   "remoteUser": "root",
 
+  // Run uv sync on container start
+  "postStartCommand": "uv sync --extra cpu",
+
   // Features to add
   "features": {
     "ghcr.io/devcontainers/features/git:1": {},

.devcontainer/dev-nvidia/devcontainer.json

@@ -0,0 +1,75 @@
+{
+  "name": "OncoLearn (NVIDIA)",
+  "dockerComposeFile": "../../docker-compose.yml",
+  "service": "dev-nvidia",
+  "runServices": ["dev-nvidia"],
+  "workspaceFolder": "/workspace",
+
+  // Configure which extensions should be installed
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "charliermarsh.ruff",
+        "ms-python.autopep8",
+        "REditorSupport.r",
+        "ms-toolsai.jupyter",
+        "ms-toolsai.vscode-jupyter-cell-tags",
+        "ms-toolsai.vscode-jupyter-slideshow",
+        "ms-azuretools.vscode-docker",
+        "tamasfe.even-better-toml"
+      ],
+      "settings": {
+        "python.defaultInterpreterPath": "/workspace/.venv/bin/python",
+        "python.terminal.activateEnvironment": true,
+        "python.analysis.autoFormatStrings": true,
+        "jupyter.notebookFileRoot": "${workspaceFolder}",
+        "terminal.integrated.defaultProfile.linux": "bash",
+        "autopep8.path": ["/workspace/.venv/bin/autopep8"],
+        "ruff.path": ["/workspace/.venv/bin/ruff"],
+        "ruff.interpreter": ["/workspace/.venv/bin/python"],
+        "[python]": {
+          "editor.tabSize": 4,
+          "editor.insertSpaces": true,
+          "editor.rulers": [120],
+          "editor.defaultFormatter": "ms-python.autopep8",
+          "editor.formatOnSave": true,
+          "editor.codeActionsOnSave": {
+            "source.fixAll": "explicit",
+            "source.organizeImports": "explicit"
+          }
+        },
+        "notebook.formatOnSave.enabled": true,
+        "notebook.codeActionsOnSave": {
+          "notebook.source.fixAll": "explicit",
+          "notebook.source.organizeImports": "explicit"
+        }
+      }
+    }
+  },
+
+  // Expose Jupyter port
+  "forwardPorts": [8888],
+  "portsAttributes": {
+    "8888": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Keep container running
+  "shutdownAction": "stopCompose",
+
+  // Run as root (can be changed for better security)
+  "remoteUser": "root",
+
+  // Run uv sync on container start
+  "postStartCommand": "uv sync --extra cu130",
+
+  // Features to add
+  "features": {
+    "ghcr.io/devcontainers/features/git:1": {},
+    "ghcr.io/devcontainers/features/github-cli:1": {}
+  }
+}

.devcontainer/pytorch-prod-amd/devcontainer.json

@@ -0,0 +1,63 @@
+{
+  "name": "OncoLearn PyTorch Production (AMD)",
+  "dockerComposeFile": "../../docker-compose.yml",
+  "service": "pytorch-prod-amd",
+  "runServices": ["pytorch-prod-amd"],
+  "workspaceFolder": "/workspace",
+
+  // Configure which extensions should be installed (minimal for production)
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "charliermarsh.ruff",
+        "tamasfe.even-better-toml"
+      ],
+      "settings": {
+        "python.defaultInterpreterPath": "/workspace/.venv/bin/python",
+        "python.terminal.activateEnvironment": true,
+        "python.analysis.autoFormatStrings": true,
+        "terminal.integrated.defaultProfile.linux": "bash",
+        "ruff.path": ["/workspace/.venv/bin/ruff"],
+        "ruff.interpreter": ["/workspace/.venv/bin/python"],
+        "[python]": {
+          "editor.tabSize": 4,
+          "editor.insertSpaces": true,
+          "editor.rulers": [120],
+          "editor.defaultFormatter": "ms-python.autopep8",
+          "editor.formatOnSave": true,
+          "editor.codeActionsOnSave": {
+            "source.fixAll": "explicit",
+            "source.organizeImports": "explicit"
+          }
+        },
+        "notebook.formatOnSave.enabled": true,
+        "notebook.codeActionsOnSave": {
+          "notebook.source.fixAll": "explicit",
+          "notebook.source.organizeImports": "explicit"
+        }
+      }
+    }
+  },
+
+  // Expose TensorBoard port
+  "forwardPorts": [6006],
+  "portsAttributes": {
+    "6006": {
+      "label": "TensorBoard",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Keep container running
+  "shutdownAction": "stopCompose",
+
+  // Run as root
+  "remoteUser": "root",
+
+  // Features to add
+  "features": {
+    "ghcr.io/devcontainers/features/git:1": {}
+  }
+}