Merge pull request #50 from voetberg/bones

Update pr with all bones updates, update linter to fix check results

.github/workflows/lint.yml

@@ -18,9 +18,9 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8
+        pip install ruff
 
     - name: Lint code
-      run: flake8 .
+      run: ruff check --fix
 
     # Add other steps as needed, such as running additional linters or formatters

src/data/data.py

@@ -14,7 +14,7 @@ def _load_simulator(self, name):
         try: 
             simulator_path = os.environ[f"{Defaults['common']['sim_location']}:{name}"]
         except KeyError as e: 
-            raise RuntimeError(f"Simulator cannot be found using env var {e}. Hint: have you registed your simulation with utils.register_simulator?")
+            raise RuntimeError(f"Simulator cannot be found using env var {e}. Hint: have you registered your simulation with utils.register_simulator?")
 
         new_class = os.path.dirname(simulator_path)
         sys.path.insert(1, new_class)

src/plots/__init__.py

@@ -1,7 +1,3 @@
-from typing import TypeVar
-from src.plots.plot import Display
-
-display = TypeVar("display", Display)
 Plots = {
 
 }

src/plots/plot.py

@@ -3,22 +3,19 @@
 import matplotlib.pyplot as plt
 from matplotlib import rcParams
 
-from src.data import data
-from src.models import model
-
-from src.utils.config import get_item, get_section
+from utils.config import get_item, get_section
 
 class Display: 
-    def __init__(self, model:model, data:data, save:bool, show:bool, out_path:Optional[str]): 
+    def __init__(self, model, data, save:bool, show:bool, out_path:Optional[str]): 
         self.save = save
         self.show = show 
         self.out_path = out_path.rstrip("/")
         if self.save: 
             assert self.out_path is not None, "out_path required to save files." 
 
-        if not os.path.exists(os.path.dirname(out_path)): 
-            os.makedirs(os.path.dirname(out_path))
-
+            if not os.path.exists(os.path.dirname(out_path)): 
+                os.makedirs(os.path.dirname(out_path))
+                
         self.model = model
         self._data_setup(data)
         self._common_settings()

src/utils/defaults.py

@@ -1,8 +1,8 @@
 Defaults = {
     "common":{
-        "out_dir":"./DeepDiagonisticsResources/results/", 
-        "temp_config": "./DeepDiagonisticsResources/temp/temp_config.yml", 
-        "sim_location": "DeepDiagonisticsResources_Simulators"
+        "out_dir":"./DeepDiagnosticsResources/results/", 
+        "temp_config": "./DeepDiagnosticsResources/temp/temp_config.yml", 
+        "sim_location": "DeepDiagnosticsResources_Simulators"
     }, 
     "model": {
         "model_engine": "SBIModel"