Update older todos.

src-tauri/src/algorithms/eval_dynamic/_trap_spaces.rs

@@ -27,7 +27,7 @@ pub fn colors_where_essential_traps(
     graph: &SymbolicAsyncGraph,
     ctx: &SymbolicSpaceContext,
 ) -> GraphColors {
-    // TODO: before computing Essential traps, restrict the colors to only the ones where all observations are trap spaces
+    // TODO: could be optimized by restricting the colors to subset where all observations are trap spaces
 
     // compute essential spaces
     let essential_traps = compute_essential_trap_spaces(graph, ctx, None);
@@ -65,8 +65,7 @@ pub fn colors_where_minimal_traps(
     graph: &SymbolicAsyncGraph,
     ctx: &SymbolicSpaceContext,
 ) -> GraphColors {
-    // TODO: before computing Minimal traps, restrict the colors to only the ones where all observations are trap spaces
-    // TODO: maybe also restrict the colors to only the ones where the observations are essential trap spaces
+    // TODO: could be optimized by restricting the colors to subset where all observations are trap spaces
 
     // compute minimal spaces
     let minimal_traps = compute_minimal_trap_spaces(graph, ctx, None);

src-tauri/src/algorithms/eval_dynamic/eval.rs

@@ -34,7 +34,7 @@ pub fn eval_dyn_prop(
         }
         ProcessedDynProp::ProcessedAttrCount(prop) => {
             // custom implementation (can be made more efficient if needed)
-            // todo: optimize - first just compute fixed-points and get colors where N_fp <= MAX_ATTR
+            // TODO: could be optimized by first computing fixed-points and removing colors where N_fp > MAX_ATTR
 
             // compute full attractors (on remaining colors) and get colors with correct n. of attrs
             let colors_per_num_attrs: Vec<GraphColors> = sort_colors_by_attr_num(graph);

src-tauri/src/algorithms/eval_dynamic/processed_props.rs

@@ -137,7 +137,7 @@ pub fn process_dynamic_props(sketch: &Sketch) -> Result<Vec<ProcessedDynProp>, S
             }
             // encode fixed-points HCTL formula
             DynPropertyType::ExistsFixedPoint(prop) => {
-                // TODO: maybe encode as multiple formulae if we have more than one observation (instead of a conjunction)?
+                // TODO: if we have whole dataset, instead of using conjunction, try encoding as multiple properties
                 let dataset_id = prop.dataset.clone().unwrap();
                 let dataset = sketch.observations.get_dataset(&dataset_id)?;
                 let formula = encode_dataset_hctl_str(
@@ -149,7 +149,7 @@ pub fn process_dynamic_props(sketch: &Sketch) -> Result<Vec<ProcessedDynProp>, S
             }
             // encode attractors with HCTL formula
             DynPropertyType::HasAttractor(prop) => {
-                // TODO: maybe encode as multiple formulae if we have more than one observation (instead of a conjunction)?
+                // TODO: if we have whole dataset, instead of using conjunction, try encoding as multiple properties
                 let dataset_id = prop.dataset.clone().unwrap();
                 let dataset = sketch.observations.get_dataset(&dataset_id)?;
                 let formula = encode_dataset_hctl_str(

src-tauri/src/algorithms/fo_logic/utils.rs

@@ -260,8 +260,6 @@ pub fn is_update_fn_symbol(fn_symbol: &str) -> bool {
 }
 
 /// Compute a valid name for an "anonymous update function" of the corresponding variable.
-///
-/// TODO: currently does not double check if there are collisions with existing params
 pub fn get_implicit_function_name(variable_name: &str) -> String {
     format!("f_{}", variable_name)
 }

src-tauri/src/sketchbook/_sketch/_impl_consistency.rs

@@ -64,7 +64,7 @@ impl Sketch {
             message += "> ISSUE: There must be at least one variable.\n";
         }
 
-        // TODO: in future, we can also add a check whether update fns match regulation monotonicity
+        // TODO: in future, we can also add a check if update fn expressions match regulation properties
 
         (consitent, message)
     }

src-tauri/src/sketchbook/_sketch/_impl_import.rs

@@ -84,7 +84,6 @@ impl Sketch {
                 let property = prop_data.to_property()?;
 
                 // ignore automatically generated static props as they were added before
-                // todo: this can loose some info as standard AEON format does not cover all regulation types
                 match prop_data.variant {
                     StatPropertyTypeData::RegulationEssential(..)
                     | StatPropertyTypeData::RegulationMonotonic(..) => {}

src-tauri/src/sketchbook/_sketch/_impl_session_state.rs

@@ -88,8 +88,7 @@ impl SessionState for Sketch {
             let mut contents = String::new();
             file.read_to_string(&mut contents)?;
 
-            // parse the AEON format
-            // TODO: aeon format currently does not support template properties and datasets
+            // parse AEON format (extended with custom annotations)
             let new_sketch = Sketch::from_aeon(&contents)?;
             self.modify_from_sketch(&new_sketch);
 

src-tauri/src/sketchbook/bn_utils.rs

@@ -3,7 +3,7 @@ use biodivine_lib_param_bn::Monotonicity as Lib_Pbn_Monotonicity;
 
 /// Utility to convert monotonicity enum used by `lib_param_bn` into the type used here.
 ///
-/// TODO: note that `lib-param-bn` currently cannot express `Dual` variant of `Monotonicity`.
+/// IMPORTANT: note that `lib-param-bn` currently cannot express `Dual` variant of `Monotonicity`.
 pub fn sign_from_monotonicity(monotonicity: Option<Lib_Pbn_Monotonicity>) -> Monotonicity {
     match monotonicity {
         Some(m) => match m {
@@ -14,23 +14,23 @@ pub fn sign_from_monotonicity(monotonicity: Option<Lib_Pbn_Monotonicity>) -> Mon
     }
 }
 
-/// Utility to convert regulation sign from enum type used in this crate into the type used in `lib_param_bn`.
+/// Utility to convert regulation sign from enum type used in this crate into the type used
+///  in `lib_param_bn`.
 ///
-/// TODO: note that `lib-param-bn` currently cannot express `Dual` variant of `Monotonicity`. We convert it
-/// to `Unknown` instead.
+/// IMPORTANT: note that `lib-param-bn` currently cannot express `Dual` variant of `Monotonicity`.
+/// We convert it to `Unknown` instead.
 pub fn sign_to_monotonicity(regulation_sign: &Monotonicity) -> Option<Lib_Pbn_Monotonicity> {
     match regulation_sign {
         Monotonicity::Activation => Some(Lib_Pbn_Monotonicity::Activation),
         Monotonicity::Inhibition => Some(Lib_Pbn_Monotonicity::Inhibition),
         Monotonicity::Unknown => None,
-        // TODO: maybe put "unimplemented" here?
         Monotonicity::Dual => None,
     }
 }
 
 /// Utility method to convert `Essentiality` from boolean.
 ///
-/// TODO: note that `lib-param-bn` currently cannot distinguish between `False` and `Unknown`
+/// IMPORTANT: note that `lib-param-bn` currently cannot distinguish between `False` and `Unknown`
 /// variants of `Essentiality`. In general, these are both represented by "false" in `lib-param-bn`.
 pub fn essentiality_from_bool(essentiality: bool) -> Essentiality {
     match essentiality {
@@ -42,7 +42,7 @@ pub fn essentiality_from_bool(essentiality: bool) -> Essentiality {
 
 /// Utility method to convert `Essentiality` into boolean.
 ///
-/// TODO: note that `lib-param-bn` currently cannot distinguish between `False` and `Unknown`
+/// IMPORTANT: note that `lib-param-bn` currently cannot distinguish between `False` and `Unknown`
 /// variants of `Essentiality`. In general, these are both represented by "false" in `lib-param-bn`.
 pub fn essentiality_to_bool(essentiality: Essentiality) -> bool {
     match essentiality {

src-tauri/src/sketchbook/layout/_node_layout.rs

@@ -10,7 +10,7 @@ use std::fmt::{Display, Error, Formatter};
 #[derive(Clone, Debug, PartialEq, Serialize, Deserialize)]
 pub struct LayoutNode {
     position: NodePosition,
-    // TODO: add other data in future (visibility, colour, shape, ...)
+    // TODO: other data layout data will be here in future (visibility, colour, shape, ...)
 }
 
 impl LayoutNode {

src-tauri/src/sketchbook/model/_model_state/_impl_editing.rs

@@ -642,7 +642,7 @@ impl ModelState {
         }
 
         // substitute id for this uninterpreted fn in all uninterpreted functions' expressions
-        // TODO: this is a bit inefficient
+        // TODO: there may be more efficient way to do this
         for fn_id in self.uninterpreted_fns.clone().keys() {
             let uninterpreted_fn = self.uninterpreted_fns.remove(fn_id).unwrap();
             let new_uninterpreted_fn = UninterpretedFn::with_substituted_fn_symbol(

src-tauri/src/sketchbook/model/_model_state/_impl_session_state/_events_layout.rs

@@ -112,7 +112,6 @@ impl ModelState {
             self.remove_layout(&layout_id)?;
             let state_change = mk_model_state_change(&["layout", "remove"], &layout_data);
 
-            // TODO: make this reversible in the future?
             Ok(Consumed::Irreversible {
                 state_change,
                 reset: true,

src-tauri/src/sketchbook/observations/_manager/_impl_session_state.rs

@@ -289,7 +289,7 @@ impl ObservationManager {
                 let new_dataset_data = DatasetData::from_dataset(&dataset_id, new_dataset);
                 let state_change = mk_obs_state_change(&["remove_var"], &new_dataset_data);
 
-                // TODO: make this potentially reversible?
+                // TODO: we can make this potentially into reversible event
                 Ok(Consumed::Irreversible {
                     state_change,
                     reset: true,
@@ -307,7 +307,7 @@ impl ObservationManager {
                 let new_dataset_data = DatasetData::from_dataset(&dataset_id, new_dataset);
                 let state_change = mk_obs_state_change(&["add_var"], &new_dataset_data);
 
-                // TODO: make this potentially reversible?
+                // TODO: we can make this potentially into reversible event
                 Ok(Consumed::Irreversible {
                     state_change,
                     reset: true,