Merge pull request #141 from apartresearch/5-set-up-rust-ci

5 set up rust ci

.github/workflows/pre-merge.yml

@@ -0,0 +1,29 @@
+name: Pre-merge
+
+on:
+  pull_request:
+    branches: [ "main", "ci-test" ]
+
+env:
+  CARGO_TERM_COLOR: always
+  RUSTFLAGS: "-Dwarnings"
+
+jobs:
+  rust:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: dtolnay/rust-toolchain@stable
+    - uses: Swatinem/rust-cache@v2
+      with:
+        prefix-key: "rust-dependencies"
+    - name: Build
+      run: cargo build --verbose
+    - name: Clippy
+      run: cargo clippy --no-deps
+    - name: Format check
+      run: cargo fmt --check
+    - name: Run tests
+      run: cargo test --verbose

python/deepdecipher/__init__.py

@@ -1,14 +1,14 @@
 from .deepdecipher import (
-    log_init,
-    start_server,
     Database,
+    DataType,
+    DataTypeHandle,
+    Index,
     ModelHandle,
     ModelMetadata,
-    DataTypeHandle,
-    DataType,
     ServiceHandle,
     ServiceProvider,
-    Index,
+    log_init,
+    start_server,
 )
 
 deepdecipher.setup_keyboard_interrupt()

rustfmt.toml

@@ -0,0 +1,4 @@
+unstable_features = true
+imports_granularity = "Crate"
+group_imports = "StdExternalCrate"
+format_strings = true

src/data/data_objects/metadata_object.rs

@@ -1,9 +1,8 @@
 use anyhow::Result;
 use serde::{Deserialize, Serialize};
 
-use crate::data::{Metadata, ModelHandle};
-
 use super::{data_object, DataObject};
+use crate::data::{Metadata, ModelHandle};
 
 #[derive(Clone, Serialize, Deserialize)]
 pub struct MetadataObject {

src/data/data_objects/neuron2graph.rs

@@ -12,9 +12,8 @@ use graphviz_rust::{
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 
-use crate::data::SimilarNeurons;
-
 use super::{data_object, DataObject};
+use crate::data::SimilarNeurons;
 
 fn id_to_str(id: &Id) -> &str {
     match id {
@@ -24,9 +23,13 @@ fn id_to_str(id: &Id) -> &str {
 
 fn id_to_usize(id: &Id) -> Result<usize> {
     let id_string = id_to_str(id);
-    id_string.parse::<usize>().with_context(|| format!(
-        "Could not parse node id {} as usize. It is assumed that all N2G graphs only use positive integer node ids.", id_string
-    ))
+    id_string.parse::<usize>().with_context(|| {
+        format!(
+            "Could not parse node id {} as usize. It is assumed that all N2G graphs only use \
+             positive integer node ids.",
+            id_string
+        )
+    })
 }
 
 fn dot_node_to_id_label_importance(node: &DotNode) -> Result<(usize, String, f32)> {
@@ -40,15 +43,26 @@ fn dot_node_to_id_label_importance(node: &DotNode) -> Result<(usize, String, f32
         .find(|Attribute(key, _)| id_to_str(key) == "label")
         .with_context(|| format!("Node with id {id} has no attribute 'label'."))?;
     // Assume that the `fillcolor` attribute is a 9 character string with '"' enclosing a hexadecimal color code.
-    let color_str = get_attribute(attributes.as_slice(), "fillcolor").with_context(|| format!(
-        "Node {id} has no attribute 'fillcolor'. It is assumed that all N2G nodes have a 'fillcolor' attribute that signifies their importance."
-    ))?;
-    let importance_hex = color_str.get(4..6).with_context(|| format!(
-            "The 'fillcolor' attribute of node {id} is insufficiently long. It is expected to be 9 characters long."
-    ))?;
-    let importance = 1.-u8::from_str_radix(importance_hex, 16).with_context(|| format!(
-        "The green part of the 'fillcolor' attribute of node {id} is not a valid hexadecimal number."
-    ))? as f32 / 255.0;
+    let color_str = get_attribute(attributes.as_slice(), "fillcolor").with_context(|| {
+        format!(
+            "Node {id} has no attribute 'fillcolor'. It is assumed that all N2G nodes have a \
+             'fillcolor' attribute that signifies their importance."
+        )
+    })?;
+    let importance_hex = color_str.get(4..6).with_context(|| {
+        format!(
+            "The 'fillcolor' attribute of node {id} is insufficiently long. It is expected to be \
+             9 characters long."
+        )
+    })?;
+    let importance = 1.
+        - u8::from_str_radix(importance_hex, 16).with_context(|| {
+            format!(
+                "The green part of the 'fillcolor' attribute of node {id} is not a valid \
+                 hexadecimal number."
+            )
+        })? as f32
+            / 255.0;
 
     let label = id_to_str(label_id).to_string();
     Ok((id, label, importance))
@@ -70,7 +84,12 @@ fn subgraph_to_nodes(subgraph: &Subgraph) -> Result<Vec<(usize, String, f32)>> {
     let id_str = id_to_str(id);
     let id: usize = id_str
         .strip_prefix("cluster_")
-        .with_context(|| format!("It is assumed that all N2G subgraphs have ids starting with 'cluster_'. Subgraph id: {id_str}"))?
+        .with_context(|| {
+            format!(
+                "It is assumed that all N2G subgraphs have ids starting with 'cluster_'. Subgraph \
+                 id: {id_str}"
+            )
+        })?
         .parse::<usize>()
         .with_context(|| format!("Failed to parse subgraph id '{id_str}' as usize."))?;
     let nodes = statements
@@ -92,16 +111,34 @@ fn dot_edge_to_ids(
 ) -> Result<(usize, usize)> {
     match edge_ty {
         EdgeTy::Pair(Vertex::N(NodeId(node_id1, _)), Vertex::N(NodeId(node_id2, _))) => {
-            let id1 = id_to_usize(node_id1).with_context(|| format!("Failed to parse first id for edge {edge_ty:?}."))?;
-            let id2 = id_to_usize(node_id2).with_context(|| format!("Failed to parse second id for edge {edge_ty:?}."))?;
+            let id1 = id_to_usize(node_id1)
+                .with_context(|| format!("Failed to parse first id for edge {edge_ty:?}."))?;
+            let id2 = id_to_usize(node_id2)
+                .with_context(|| format!("Failed to parse second id for edge {edge_ty:?}."))?;
             match get_attribute(attributes, "dir") {
                 Some("back") => Ok((id2, id1)),
-                None => bail!("No direction attribute found for edge {id1}->{id2}. It is assumed that all N2G graphs only use edges with direction 'back'."),
-                _ => bail!("Only edges with direction 'back' or 'forward' are supported. It is assumed that all N2G graphs only use edges with direction 'back' or 'forward'. Edge: {:?}", edge_ty)
+                None => bail!(
+                    "No direction attribute found for edge {id1}->{id2}. It is assumed that all \
+                     N2G graphs only use edges with direction 'back'."
+                ),
+                _ => bail!(
+                    "Only edges with direction 'back' or 'forward' are supported. It is assumed \
+                     that all N2G graphs only use edges with direction 'back' or 'forward'. Edge: \
+                     {:?}",
+                    edge_ty
+                ),
             }
         }
-        EdgeTy::Pair(_, _) => bail!("Only edges between individual nodes are supported. It is assumed that N2G does not use edges between subgraphs. Edge: {:?}", edge_ty),
-        EdgeTy::Chain(_) => bail!("Only pair edges are supported. It is assumed that all N2G graphs only use pair edges. Edge: {:?}", edge_ty)
+        EdgeTy::Pair(_, _) => bail!(
+            "Only edges between individual nodes are supported. It is assumed that N2G does not \
+             use edges between subgraphs. Edge: {:?}",
+            edge_ty
+        ),
+        EdgeTy::Chain(_) => bail!(
+            "Only pair edges are supported. It is assumed that all N2G graphs only use pair \
+             edges. Edge: {:?}",
+            edge_ty
+        ),
     }
 }
 

src/data/data_objects/neuroscope/neuroscope_page.rs

@@ -4,7 +4,6 @@ use anyhow::{bail, Context, Result};
 use itertools::Itertools;
 use regex::Regex;
 use serde::{Deserialize, Serialize};
-
 use utoipa::ToSchema;
 
 use crate::data::{

src/data/database/data_types/json.rs

@@ -1,5 +1,7 @@
+use anyhow::{bail, Context, Result};
 use async_trait::async_trait;
 
+use super::{data_type::DataValidationError, DataTypeDiscriminants, ModelDataType};
 use crate::{
     data::{
         data_objects::{DataObject, JsonData},
@@ -8,10 +10,6 @@ use crate::{
     Index,
 };
 
-use super::{data_type::DataValidationError, DataTypeDiscriminants, ModelDataType};
-
-use anyhow::{bail, Context, Result};
-
 pub struct Json {
     model: ModelHandle,
     data_type: DataTypeHandle,
@@ -81,26 +79,42 @@ impl Json {
     pub async fn layer_page(&self, layer_index: u32) -> Result<JsonData> {
         let model_name = self.model.name();
         let data_type_name = self.data_type.name();
-        let raw_data = self.model
-            .layer_data( &self.data_type, layer_index)
-            .await.with_context(|| {
-                format!("Failed to get '{data_type_name}' layer data for layer {layer_index} in model '{model_name}'.")
+        let raw_data = self
+            .model
+            .layer_data(&self.data_type, layer_index)
+            .await
+            .with_context(|| {
+                format!(
+                    "Failed to get '{data_type_name}' layer data for layer {layer_index} in model \
+                     '{model_name}'."
+                )
             })?
             .with_context(|| {
-                format!("Database has no '{data_type_name}' layer data for layer {layer_index} in model '{model_name}'.")
+                format!(
+                    "Database has no '{data_type_name}' layer data for layer {layer_index} in \
+                     model '{model_name}'."
+                )
             })?;
         JsonData::from_binary(raw_data.as_slice())
     }
     pub async fn neuron_page(&self, layer_index: u32, neuron_index: u32) -> Result<JsonData> {
         let model_name = self.model.name();
         let data_type_name = self.data_type.name();
-        let raw_data = self.model
-            .neuron_data( &self.data_type, layer_index, neuron_index)
-            .await.with_context(|| {
-                format!("Failed to get '{data_type_name}' neuron data for neuron l{layer_index}n{neuron_index} in model '{model_name}'.")
+        let raw_data = self
+            .model
+            .neuron_data(&self.data_type, layer_index, neuron_index)
+            .await
+            .with_context(|| {
+                format!(
+                    "Failed to get '{data_type_name}' neuron data for neuron \
+                     l{layer_index}n{neuron_index} in model '{model_name}'."
+                )
             })?
             .with_context(|| {
-                format!("Database has no '{data_type_name}' neuron data for neuron l{layer_index}n{neuron_index} in model '{model_name}'.")
+                format!(
+                    "Database has no '{data_type_name}' neuron data for neuron \
+                     l{layer_index}n{neuron_index} in model '{model_name}'."
+                )
             })?;
         JsonData::from_binary(raw_data.as_slice())
     }

src/data/database/data_types/neuron2graph.rs

@@ -1,13 +1,12 @@
 use anyhow::{bail, Context, Result};
 use async_trait::async_trait;
 
+use super::{data_type::DataValidationError, DataTypeDiscriminants, ModelDataType};
 use crate::data::{
     data_objects::{DataObject, Graph},
     DataTypeHandle, ModelHandle,
 };
 
-use super::{data_type::DataValidationError, DataTypeDiscriminants, ModelDataType};
-
 pub struct Neuron2Graph {
     model: ModelHandle,
     data_type: DataTypeHandle,
@@ -47,12 +46,21 @@ impl ModelDataType for Neuron2Graph {
 impl Neuron2Graph {
     pub async fn neuron_graph(&self, layer_index: u32, neuron_index: u32) -> Result<Graph> {
         let model_name = self.model.name();
-        let raw_data = self.model
+        let raw_data = self
+            .model
             .neuron_data(&self.data_type, layer_index, neuron_index)
             .await?
             .with_context(|| {
-                format!("Database has no neuron2graph data for neuron l{layer_index}n{neuron_index} in model '{model_name}'")
+                format!(
+                    "Database has no neuron2graph data for neuron l{layer_index}n{neuron_index} \
+                     in model '{model_name}'"
+                )
             })?;
-        Graph::from_binary(raw_data).with_context(|| format!("Failed to unpack neuron2graph graph for neuron l{layer_index}n{neuron_index} in model '{model_name}'."))
+        Graph::from_binary(raw_data).with_context(|| {
+            format!(
+                "Failed to unpack neuron2graph graph for neuron l{layer_index}n{neuron_index} in \
+                 model '{model_name}'."
+            )
+        })
     }
 }

src/data/database/data_types/neuron_explainer.rs

@@ -1,17 +1,16 @@
 use anyhow::{bail, Context, Result};
 use async_trait::async_trait;
 
+use super::{
+    data_type::{DataValidationError, ModelDataType},
+    DataTypeDiscriminants,
+};
 use crate::data::{
     data_objects::{DataObject, NeuronExplainerPage},
     database::ModelHandle,
     DataTypeHandle,
 };
 
-use super::{
-    data_type::{DataValidationError, ModelDataType},
-    DataTypeDiscriminants,
-};
-
 pub struct NeuronExplainer {
     model: ModelHandle,
     data_type: DataTypeHandle,
@@ -55,14 +54,25 @@ impl NeuronExplainer {
         neuron_index: u32,
     ) -> Result<Option<NeuronExplainerPage>> {
         let model_name = self.model.name();
-        let raw_data = self.model
-            .neuron_data( &self.data_type, layer_index, neuron_index)
-            .await.with_context(|| {
-                format!("Failed to get neuron explainer neuron data for neuron l{layer_index}n{neuron_index} in model '{model_name}'.")
-            })?;
-        raw_data.map(|raw_data| NeuronExplainerPage::from_binary(raw_data.as_slice())
+        let raw_data = self
+            .model
+            .neuron_data(&self.data_type, layer_index, neuron_index)
+            .await
             .with_context(|| {
-                format!("Failed to deserialize neuron explainer neuron data for neuron l{layer_index}n{neuron_index} in model '{model_name}'.")
-            })).transpose()
+                format!(
+                    "Failed to get neuron explainer neuron data for neuron \
+                     l{layer_index}n{neuron_index} in model '{model_name}'."
+                )
+            })?;
+        raw_data
+            .map(|raw_data| {
+                NeuronExplainerPage::from_binary(raw_data.as_slice()).with_context(|| {
+                    format!(
+                        "Failed to deserialize neuron explainer neuron data for neuron \
+                         l{layer_index}n{neuron_index} in model '{model_name}'."
+                    )
+                })
+            })
+            .transpose()
     }
 }