all\refac: #68 use tfds

- general refactor for preffering usage of tfds
- use ruff for formatting and linting
- update contribution docs

Author: blotero

.github/workflows/python-ci.yml

@@ -72,12 +72,13 @@ jobs:
       - name: Run mypy
         run: |
           cd core
-          poetry run mypy seg_tgce
+          poetry run mypy .
 
-      - name: Run pylint
+      - name: Run linter
         run: |
           cd core
-          poetry run pylint seg_tgce
+          poetry run ruff check .
+          poetry run ruff format --exit-non-zero-on-format .
 
   lint-docs:
     runs-on: ubuntu-22.04

.gitignore

@@ -10,4 +10,5 @@ notebooks/**/.ipynb_checkpoints
 core/dist
 __data__
 **/results/**
-tuner_results/
+tuner_results/
+**/vis/

.vscode/launch.json

@@ -4,6 +4,7 @@
     // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
     "version": "0.2.0",
     "configurations": [
+    
         {
             "name": "Poetry: Oxford pet",
             "type": "debugpy",
@@ -48,13 +49,26 @@
                 "PYTHONPATH": "${workspaceFolder}"
             }
         },
+        {
+            "name": "Poetry: Histology baseline experiment",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "seg_tgce.experiments.histology.baseline",
+            "console": "integratedTerminal",
+            "justMyCode": true,
+            "env": {
+                "PYTHONPATH": "${workspaceFolder}"
+            },
+            // "args": ["--use-tuner"],
+        },
         {
             "name": "Poetry: Histology scalar experiment",
             "type": "debugpy",
             "request": "launch",
             "module": "seg_tgce.experiments.histology.scalar",
             "console": "integratedTerminal",
             "justMyCode": true,
+            "args": ["--use-tuner"],
             "env": {
                 "PYTHONPATH": "${workspaceFolder}"
             }
@@ -92,6 +106,17 @@
                 "PYTHONPATH": "${workspaceFolder}"
             }
         },
+        {
+            "name": "Poetry: Crowd seg tfds",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "seg_tgce.data.crowd_seg.tfds_builder",
+            "console": "integratedTerminal",
+            "justMyCode": true,
+            "env": {
+                "PYTHONPATH": "${workspaceFolder}"
+            }
+        },
         {
             "name": "Poetry: Unet",
             "type": "debugpy",
@@ -124,6 +149,28 @@
             "env": {
                 "PYTHONPATH": "${workspaceFolder}"
             }
-        }
+        },
+        {
+            "name": "Tgce scalar debug",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "seg_tgce.loss.tgce_debug",
+            "console": "integratedTerminal",
+            "justMyCode": true,
+            "env": {
+                "PYTHONPATH": "${workspaceFolder}"
+            }
+        },
+        {
+            "name": "Poetry: Oxford pet tfds",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "seg_tgce.data.oxford_pet.oxford_pet_tfds",
+            "console": "integratedTerminal",
+            "justMyCode": true,
+            "env": {
+                "PYTHONPATH": "${workspaceFolder}"
+            }
+        },
     ]
 }

.vscode/settings.json

@@ -1,19 +1,20 @@
 {
   "editor.formatOnSave": true,
-  "editor.rulers": [88],
+  "editor.rulers": [90],
   "python.analysis.autoImportCompletions": true,
   "[json]": {
     "editor.defaultFormatter": "esbenp.prettier-vscode",
-    "editor.formatOnSave": true
+    "editor.formatOnSave": true,
   },
   "[python]": {
-    "editor.defaultFormatter": "ms-python.black-formatter",
+    "editor.defaultFormatter": "charliermarsh.ruff",
     "editor.formatOnSave": true,
     "editor.codeActionsOnSave": {
-      "source.organizeImports": "explicit"
+      "source.organizeImports": "explicit",
+      "source.fixAll": "explicit"
     }
   },
-  "isort.args": ["--profile", "black"],
-  "isort.path": ["~/.env/python", "-m", "isort"],
-  "workbench.colorTheme": "Gruvbox Dark Hard"
+  "workbench.colorTheme": "Gruvbox Dark Hard",
+  "mypy-type-checker.cwd": "${nearestConfig}",
+  "python.defaultInterpreterPath": "${workspaceFolder}/core/.venv/bin/python"
 }