Merge pull request #207 from noamteyssier/206-add-colored-help

206 add colored help
noamteyssier · Oct 8, 2024 · 932393e · 932393e
2 parents ebbff85 + 58ce6ca
commit 932393e
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Showing 3 changed files with 29 additions and 22 deletions.
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "ggetrs"
-version = "0.1.83"
+version = "0.1.84"
 edition = "2021"
 license = "MIT"
 description = "Efficient querying of biological databases from the command line"
@@ -21,7 +21,7 @@ default = ["pyo3/extension-module"]
 [dependencies]
 anyhow = "1.0.64"
 bitvec = "1.0.1"
-bon = "2.1.1"
+bon = "2.3.0"
 chrono = "0.4.22"
 clap = { version = "4.0.18", features = ["derive"] }
 clap_complete = "4.0.3"
@@ -33,10 +33,10 @@ polars = { version = "0.43.1", default-features = false, features = ["json"] }
 pyo3 = { version = "0.22.2", features = ["extension-module", "anyhow"] }
 regex = "1.6.0"
 reqwest = { version = "0.12.5", features = [
-  "json",
-  "multipart",
-  "blocking",
-  "stream",
+    "json",
+    "multipart",
+    "blocking",
+    "stream",
 ] }
 serde = { version = "1.0.144", features = ["derive"] }
 serde-xml-rs = "0.6.0"

diff --git a/src/cli/cli.rs b/src/cli/cli.rs
@@ -5,10 +5,24 @@ use crate::{
     blast::types::{BlastDatabase, BlastProgram},
     ensembl::ENSEMBL_RELEASE_STR,
 };
-use clap::{Parser, Subcommand};
+use clap::{
+    builder::{
+        styling::{AnsiColor, Effects},
+        Styles,
+    },
+    Parser, Subcommand,
+};
 use clap_complete::Shell;
 
+// Configures Clap v3-style help menu colors
+const STYLES: Styles = Styles::styled()
+    .header(AnsiColor::Green.on_default().effects(Effects::BOLD))
+    .usage(AnsiColor::Green.on_default().effects(Effects::BOLD))
+    .literal(AnsiColor::Cyan.on_default().effects(Effects::BOLD))
+    .placeholder(AnsiColor::Cyan.on_default());
+
 #[derive(Parser)]
+#[command(styles = STYLES)]
 #[clap(author, version, about)]
 #[clap(propagate_version = true)]
 pub struct Cli {

diff --git a/src/cli/string.rs b/src/cli/string.rs
@@ -3,7 +3,7 @@ use crate::{
     utils::{match_output, OutputFormat},
 };
 use anyhow::Result;
-use bon::builder;
+use bon::{builder, Builder};
 use clap::{Parser, Subcommand};
 use serde_json::{json, Value};
 use std::io::Write;
@@ -85,8 +85,7 @@ impl OutputArgs {
     }
 }
 
-#[derive(Debug, Clone, Parser)]
-#[builder]
+#[derive(Debug, Clone, Parser, Builder)]
 #[clap(next_help_heading = "STRING Network Arguments")]
 /// Retrieves the network interactions for your input protein(s) in various text based formats
 pub struct StringNetworkArgs {
@@ -146,8 +145,7 @@ impl StringNetworkArgs {
     }
 }
 
-#[derive(Debug, Clone, Parser)]
-#[builder]
+#[derive(Debug, Clone, Parser, Builder)]
 #[clap(next_help_heading = "STRING Homology Arguments")]
 pub struct StringHomologyArgs {
     /// List of genes to retrieve network for
@@ -175,8 +173,7 @@ impl StringHomologyArgs {
     }
 }
 
-#[derive(Debug, Clone, Parser)]
-#[builder]
+#[derive(Debug, Clone, Parser, Builder)]
 #[clap(next_help_heading = "STRING Mapping Identifiers Arguments")]
 pub struct StringMappingArgs {
     /// List of genes to retrieve network for
@@ -219,8 +216,7 @@ impl StringMappingArgs {
 }
 
 /// Gets all the STRING interaction partners of your proteins
-#[derive(Debug, Clone, Parser)]
-#[builder]
+#[derive(Debug, Clone, Parser, Builder)]
 #[clap(next_help_heading = "STRING Interactions Arguments")]
 pub struct StringInteractionsArgs {
     /// List of genes to retrieve network for
@@ -271,8 +267,7 @@ impl StringInteractionsArgs {
 }
 
 /// Performs the enrichment analysis of your set of proteins for the Gene Ontology, KEGG pathways, UniProt Keywords, PubMed publications, Pfam, InterPro and SMART domains.
-#[derive(Debug, Clone, Parser)]
-#[builder]
+#[derive(Debug, Clone, Parser, Builder)]
 #[clap(next_help_heading = "STRING Functional Enrichment Arguments")]
 pub struct StringFunctionalEnrichmentArgs {
     /// List of genes to retrieve network for
@@ -310,8 +305,7 @@ impl StringFunctionalEnrichmentArgs {
 }
 
 /// Gets the functional annotation (Gene Ontology, UniProt Keywords, PFAM, INTERPRO and SMART domains) of your list of proteins.
-#[derive(Debug, Clone, Parser)]
-#[builder]
+#[derive(Debug, Clone, Parser, Builder)]
 #[clap(next_help_heading = "STRING Functional Annotations Arguments")]
 pub struct StringFunctionalAnnotationArgs {
     /// List of genes to retrieve network for
@@ -352,8 +346,7 @@ impl StringFunctionalAnnotationArgs {
 }
 
 /// Tests if your network has more interactions than expected
-#[derive(Debug, Clone, Parser)]
-#[builder]
+#[derive(Debug, Clone, Parser, Builder)]
 #[clap(next_help_heading = "STRING PPI Enrichment Arguments")]
 pub struct StringPpiEnrichmentArgs {
     /// List of genes to retrieve network for