feat: implement shellcheck lints in command blocks (#191)

.github/actions/install-shellcheck/action.yaml

@@ -0,0 +1,28 @@
+name: Install ShellCheck
+description: "Installs ShellCheck. Supports Ubuntu, macOS, and Windows."
+runs:
+  using: "composite"
+  steps:
+    - uses: awalsh128/cache-apt-pkgs-action@latest
+      if: runner.os == 'Linux'
+      run:
+        gh release download -R koalaman/shellcheck -p 'shellcheck-v*.linux.x86_64.tar.xz' -O shellcheck-latest.tar.xz
+        tar -xvf shellcheck-latest.tar.xz
+        chmod +x ./shellcheck
+        echo ${{github.workspace}} >> "$GITHUB_PATH"
+        export PATH="$PATH":"$(pwd)"
+    - name: install shellcheck -- macOS
+      shell: bash
+      if: runner.os == 'macOS'
+      run: |
+        gh release download -R koalaman/shellcheck -p 'shellcheck-v*.darwin.aarch64.tar.xz' -O shellcheck-latest.tar.xz
+        tar -xvf shellcheck-latest.tar.xz
+        chmod +x ./shellcheck
+        echo ${{github.workspace}} >> "$GITHUB_PATH"
+    - name: install shellcheck -- Windows
+      if: runner.os == 'Windows'
+      shell: powershell
+      run: |
+        gh release download -R koalaman/shellcheck -p 'shellcheck-v*.zip' -O shellcheck-latest.zip
+        7z x shellcheck-latest.zip
+        Add-Content $env:GITHUB_PATH "$(Get-Location).Path"

Cargo.toml

@@ -47,6 +47,7 @@ parking_lot = "0.12.3"
 path-clean = "1.0.1"
 petgraph = "0.6.5"
 pretty_assertions = "1.4.0"
+rand = "0.8.5"
 rayon = "1.10.0"
 regex = "1.11.1"
 reqwest = { version = "0.12.5", default-features = false, features = ["rustls-tls", "http2", "charset"] }

gauntlet/CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+* `--shellcheck` flag to run shellcheck lints in both standard and arena modes ([#264](https://github.com/stjude-rust-labs/wdl/pull/264))
 * Full analysis instead of basic validation ([#207](https://github.com/stjude-rust-labs/wdl/pull/172))
 * Checkout submodules ([#207](https://github.com/stjude-rust-labs/wdl/pull/172))
 

gauntlet/src/lib.rs

@@ -44,6 +44,7 @@ use wdl::analysis::rules;
 use wdl::ast::Diagnostic;
 use wdl::lint::LintVisitor;
 use wdl::lint::ast::Validator;
+use wdl::lint::rules::ShellCheckRule;
 
 use crate::repository::WorkDir;
 
@@ -124,6 +125,10 @@ pub struct Args {
     /// Additional information is logged in the console.
     #[arg(short, long)]
     pub verbose: bool,
+
+    /// Enable shellcheck lints.
+    #[arg(long, action)]
+    pub shellcheck: bool,
 }
 
 /// Main function for this subcommand.
@@ -185,6 +190,9 @@ pub async fn gauntlet(args: Args) -> Result<()> {
                 if args.arena {
                     validator.add_visitor(LintVisitor::default());
                 }
+                if args.shellcheck {
+                    validator.add_visitor(ShellCheckRule);
+                }
 
                 validator
             },

wdl-lint/CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Added
 
+* Added a `ShellCheck` rule ([#264](https://github.com/stjude-rust-labs/wdl/pull/264)).
 * Added a `RedundantInputAssignment` rule ([#244](https://github.com/stjude-rust-labs/wdl/pull/244)).
 
 ## Changed

wdl-lint/Cargo.toml

@@ -13,9 +13,14 @@ readme = "../README.md"
 
 [dependencies]
 wdl-ast = { path = "../wdl-ast", version = "0.9.0" }
+anyhow = { workspace = true }
 convert_case = { workspace = true }
 indexmap = { workspace = true }
+rand = { workspace = true }
 rowan = { workspace = true }
+serde = { workspace = true }
+serde_json = { workspace = true }
+tracing = { workspace = true }
 
 [dev-dependencies]
 codespan-reporting = { workspace = true }

wdl-lint/RULES.md

@@ -43,6 +43,7 @@ be out of sync with released packages.
 | `RuntimeSectionKeys`             | Completeness, Deprecated      | Ensures that runtime sections have the appropriate keys.                                          |
 | `RedundantInputAssignment`       | Style                         | Ensures that redundant input assignments are shortened                                            |
 | `SectionOrdering`                | Sorting, Style                | Ensures that sections within tasks and workflows are sorted.                                      |
+| `ShellCheck`                     | Correctness, Portability      | (BETA) Ensures that command sections are free of shellcheck diagnostics.                          |
 | `SnakeCase`                      | Clarity, Naming, Style        | Ensures that tasks, workflows, and variables are defined with snake_case names.                   |
 | `Todo`                           | Completeness                  | Ensures that `TODO` statements are flagged for followup.                                          |
 | `TrailingComma`                  | Style                         | Ensures that lists and objects in meta have a trailing comma.                                     |

wdl-lint/src/lib.rs

@@ -29,6 +29,8 @@
 #![warn(clippy::missing_docs_in_private_items)]
 #![warn(rustdoc::broken_intra_doc_links)]
 
+use std::collections::HashSet;
+
 use wdl_ast::Diagnostics;
 use wdl_ast::SyntaxKind;
 use wdl_ast::Visitor;
@@ -150,3 +152,33 @@ pub fn rules() -> Vec<Box<dyn Rule>> {
 
     rules
 }
+
+/// Gets the optional rule set.
+pub fn optional_rules() -> Vec<Box<dyn Rule>> {
+    let opt_rules: Vec<Box<dyn Rule>> = vec![Box::<rules::ShellCheckRule>::default()];
+
+    // Ensure all the rule ids are unique and pascal case
+    #[cfg(debug_assertions)]
+    {
+        use convert_case::Case;
+        use convert_case::Casing;
+
+        use crate::rules;
+        let mut set: HashSet<&str> = HashSet::from_iter(rules().iter().map(|r| r.id()));
+        for r in opt_rules.iter() {
+            if r.id().to_case(Case::Pascal) != r.id() {
+                panic!("lint rule id `{id}` is not pascal case", id = r.id());
+            }
+
+            if !set.insert(r.id()) {
+                panic!("duplicate rule id `{id}`", id = r.id());
+            }
+
+            if RESERVED_RULE_IDS.contains(&r.id()) {
+                panic!("rule id `{id}` is reserved", id = r.id());
+            }
+        }
+    }
+
+    opt_rules
+}

wdl-lint/src/rules.rs

@@ -35,6 +35,7 @@ mod preamble_formatting;
 mod redundant_input_assignment;
 mod runtime_section_keys;
 mod section_order;
+mod shellcheck;
 mod snake_case;
 mod todo;
 mod trailing_comma;
@@ -77,6 +78,7 @@ pub use preamble_formatting::*;
 pub use redundant_input_assignment::*;
 pub use runtime_section_keys::*;
 pub use section_order::*;
+pub use shellcheck::*;
 pub use snake_case::*;
 pub use todo::*;
 pub use trailing_comma::*;

wdl-lint/src/rules/misplaced_lint_directive.rs

@@ -17,9 +17,11 @@ use wdl_ast::ToSpan;
 use wdl_ast::VisitReason;
 use wdl_ast::Visitor;
 
+use super::ShellCheckRule;
 use crate::Rule;
 use crate::Tag;
 use crate::TagSet;
+use crate::optional_rules;
 use crate::rules;
 
 /// The identifier for the unknown rule rule.
@@ -60,6 +62,10 @@ pub static RULE_MAP: LazyLock<HashMap<&'static str, Option<&'static [SyntaxKind]
         for rule in rules() {
             map.insert(rule.id(), rule.exceptable_nodes());
         }
+        // insert optional rules as well
+        for rule in optional_rules() {
+            map.insert(rule.id(), rule.exceptable_nodes());
+        }
         map
     });