Maintenance: resolve #8, update links, pre-commit cleanup

.gitattributes

@@ -0,0 +1 @@
+*.html linguist-vendored

.gitignore

@@ -13,4 +13,9 @@ AppData
 *.txt
 *.DS_Store
 *.csv
-*._*
+*._*
+
+/data/zenodo
+
+/data/processed/*.pkl
+/data/processed/*.pdf

.pre-commit-config.yaml

@@ -1,21 +1,21 @@
 repos:
-  - repo: https://github.com/astral-sh/ruff-pre-commit  
-    rev: v0.6.8  # Make sure you're using the correct version of Ruff
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.2 # Make sure you're using the correct version of Ruff
     hooks:
-    # Run the linter.
+      # Run the linter.
       - id: ruff
-        types_or: [ python, pyi ]  # Target Python files and type stub files
-        args: ['check', '--select', 'I', '--fix', '.']
-    # Run the formatter.
+        types_or: [python, pyi] # Target Python files and type stub files
+        args: ["check", "--select", "I", "--fix", "."]
+      # Run the formatter.
       - id: ruff-format
-        types_or: [ python, pyi ]  # Format Python and stub files
+        types_or: [python, pyi] # Format Python and stub files
 
   # Mypy type checker
   - repo: local
     hooks:
       - id: mypy
         name: Analyze with Mypy
-        entry: mypy --strict  # Runs Mypy with the strictest settings
+        entry: mypy --strict # Runs Mypy with the strictest settings
         language: python
-        types: ['python']  # Targets Python files
-        files: \.py$  # Only .py files
+        types: ["python"] # Targets Python files
+        files: \.py$ # Only .py files

app.py

@@ -30,12 +30,8 @@
 
     if selected_tab == "Trajectories":
         msg = st.empty()
-        file_name_to_path = {
-            path.split("/")[-1]: path for path in st.session_state.files
-        }
-        filename = str(
-            st.selectbox(":open_file_folder: **Select a file**", file_name_to_path)
-        )
+        file_name_to_path = {path.split("/")[-1]: path for path in st.session_state.files}
+        filename = str(st.selectbox(":open_file_folder: **Select a file**", file_name_to_path))
         st.session_state.selected_file = file_name_to_path[filename]
         run_tab2(file_name_to_path[filename], msg)
 
@@ -52,11 +48,7 @@
     #     run_explorer()
 
     if selected_tab == "Geometry":
-        file_name_to_path = {
-            path.split("/")[-1]: path for path in st.session_state.files
-        }
-        filename = str(
-            st.selectbox(":open_file_folder: **Select a file**", file_name_to_path)
-        )
+        file_name_to_path = {path.split("/")[-1]: path for path in st.session_state.files}
+        filename = str(st.selectbox(":open_file_folder: **Select a file**", file_name_to_path))
         st.session_state.selected_file = file_name_to_path[filename]
         run_tab_animation(file_name_to_path[filename])