Rename crate zefiro-core -> zefiro-pipeline

.github/workflows/cd.yml

@@ -33,12 +33,12 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
       - name: Verify package
-        run: cargo verify-project --manifest-path zefiro-core/zefiro-core-cwl/Cargo.toml
+        run: cargo verify-project --manifest-path zefiro-core/zefiro-cwl-parser/Cargo.toml
       - name: Set the release version
         run: echo "RELEASE_VERSION=${GITHUB_REF:11}" >> "$GITHUB_ENV"
       - name: Install Rust toolchain
         uses: dtolnay/rust-toolchain@stable
-      - name: Publish the zefiro-core-cwl library
+      - name: Publish the zefiro-cwl-parser library
         run: |
-          cargo publish --manifest-path zefiro-core/zefiro-core-cwl/Cargo.toml \
+          cargo publish --manifest-path zefiro-core/zefiro-cwl-parser/Cargo.toml \
             --locked --token ${{ secrets.CARGO_REGISTRY_TOKEN }}

Cargo.toml

@@ -6,7 +6,7 @@ edition = "2021"
 [workspace]
 members = [
     "zefiro-cli",
-    "zefiro-core",
-    "zefiro-core/zefiro-core-cwl",
+    "zefiro-pipeline",
+    "zefiro-pipeline/zefiro-cwl-parser",
     "zefiro-ui"
 ]

README.md

@@ -1,3 +1,5 @@
 **Code**: [![codecov](https://codecov.io/gh/zefiroproj/zefiro/graph/badge.svg?token=5DgmM1KzuQ)](https://codecov.io/gh/zefiroproj/zefiro)
 
-# Zefiro - fast, scalable and simple engine to manage workflows
+# Zefiro - fast, scalable and simple engine to manage workflows
+
+⚠️ This project is a Work In Progress, and is very far from being suitable for use ⚠️

release.sh

@@ -36,11 +36,11 @@ export GIT_CLIFF_TEMPLATE="\
 		- {% if commit.breaking %}(breaking) {% endif %}{{ commit.message | upper_first }} ({{ commit.id | truncate(length=7, end=\"\") }})\
 	{% endfor %}
 	{% endfor %}"
-if [ ! -f "examples/detailed.toml" ]; then
-	echo "Error: examples/detailed.toml not found"
+if [ ! -f "test_data/detailed.toml" ]; then
+	echo "Error: test_data/detailed.toml not found"
 	exit 1
 fi
-changelog=$(git cliff --config examples/detailed.toml --unreleased --strip all)
+changelog=$(git cliff --config test_data/detailed.toml --unreleased --strip all)
 
 # create a signed tag
 git -c user.name="zefiro" \

zefiro-core/zefiro-core-cwl/Cargo.toml → zefiro-pipeline/zefiro-cwl-parser/Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-name = "zefiro-core-cwl"
+name = "zefiro-cwl-parser"
 version = "0.1.0"
 description = """
 "The Common Workflow Language (CWL) object model that used in `zefiro`.

zefiro-core/zefiro-core-cwl/README.md → zefiro-pipeline/zefiro-cwl-parser/README.md

@@ -1,4 +1,4 @@
-# zefiro-core-cwl
+# zefiro-cwl-parser
 
 A Rust library for parsing and working with Common Workflow Language (CWL) documents.
 
@@ -13,18 +13,18 @@ Add this to your `Cargo.toml`:
 
 ```toml
 [dependencies]
-zefiro-core-cwl = "0.1.0"
+zefiro-cwl-parser = "0.1.0"
 ```
 
 
 ### How to parse CWL Schema document?
 
 ```rust
-use zefiro_core_cwl::CwlSchema;
+use zefiro_cwl_parser::CwlSchema;
 
 fn main() -> Result<(), Box<dyn std::error::Error>> {
   // Parse from file
-  let schema = CwlSchema::from_path("examples/cwl/clt-step-schema.yml").unwrap();
+  let schema = CwlSchema::from_path("test_data/cwl/clt-step-schema.yml").unwrap();
 
   // Parse from string
   let yaml_str = r#"
@@ -65,12 +65,12 @@ fn main() -> Result<(), Box<dyn std::error::Error>> {
 ### How to parse CWL Values document?
 
 ```rust
-use zefiro_core_cwl::CwlValues;
+use zefiro_cwl_parser::CwlValues;
 
 
 fn main() -> Result<(), Box<dyn std::error::Error>> {
   // Parse input values from file
-  let values = CwlValues::from_path("examples/cwl/clt-step-values.yml").unwrap();
+  let values = CwlValues::from_path("test_data/cwl/clt-step-values.yml").unwrap();
 
   // Create values from string
   let yaml_input = r#"

zefiro-core/zefiro-core-cwl/src/schema/document.rs → zefiro-pipeline/zefiro-cwl-parser/src/schema/document.rs

@@ -25,9 +25,9 @@ impl CwlSchema {
     /// Deserializes YAML `file` containing CWL values into CwlSchema structure.
     ///
     /// ```
-    /// use zefiro_core_cwl::schema::document::CwlSchema;
+    /// use zefiro_cwl_parser::schema::document::CwlSchema;
     ///
-    /// let yaml_file = "examples/cwl/clt-step-schema.yml";
+    /// let yaml_file = "test_data/cwl/clt-step-schema.yml";
     ///
     /// let values = CwlSchema::from_path(yaml_file).expect("Failed to deserialize CWL values document");
     /// ```
@@ -61,7 +61,7 @@ impl CwlSchema {
     ///
     /// ```
     /// use serde_yaml::Value;
-    /// use zefiro_core_cwl::schema::document::CwlSchema;
+    /// use zefiro_cwl_parser::schema::document::CwlSchema;
     ///
     /// let yaml_str = r#"
     /// cwlVersion: v1.2
@@ -106,11 +106,11 @@ impl CwlSchema {
 
     /// Serializes CwlSchema structure and writes it into `file`.
     /// ```
-    /// use zefiro_core_cwl::schema::document::CwlSchema;
+    /// use zefiro_cwl_parser::schema::document::CwlSchema;
     /// use std::fs::File;
     /// use std::io::BufWriter;
     ///
-    /// let yaml_file = "examples/cwl/clt-step-schema.yml";
+    /// let yaml_file = "test_data/cwl/clt-step-schema.yml";
     /// let schema = CwlSchema::from_path(yaml_file).expect("Failed to serialize CWL schema document");
     /// let mut tmpfile = tempfile::tempfile().unwrap();
     /// let mut writer = BufWriter::new(tmpfile);
@@ -137,15 +137,15 @@ mod tests {
     use std::io::{Error, ErrorKind, Write};
 
     #[rstest]
-    #[case("examples/cwl/clt-step-schema.yml")]
-    #[case("examples/cwl/wf-step-schema.yml")]
+    #[case("test_data/cwl/clt-step-schema.yml")]
+    #[case("test_data/cwl/wf-step-schema.yml")]
     fn test_cwlschema_from_path(#[case] file_path: &str) {
         CwlSchema::from_path(file_path).expect("Failed to deserialize CWL schema document");
     }
 
     #[rstest]
-    #[case("examples/cwl/clt-step-schema.yml")]
-    #[case("examples/cwl/wf-step-schema.yml")]
+    #[case("test_data/cwl/clt-step-schema.yml")]
+    #[case("test_data/cwl/wf-step-schema.yml")]
     fn test_cwlschema_to_yaml(#[case] file_path: &str) {
         let values = CwlSchema::from_path(file_path).expect("Failed to deserialize CWL schema");
         let temp_file = tempfile::NamedTempFile::new().unwrap();

zefiro-core/zefiro-core-cwl/src/values/document.rs → zefiro-pipeline/zefiro-cwl-parser/src/values/document.rs

@@ -28,8 +28,8 @@ impl CwlValues {
     /// Deserializes YAML `file` containing CWL values into CwlValues structure.
     ///
     /// ```
-    /// use zefiro_core_cwl::values::document::CwlValues;
-    /// let yaml_file = "examples/cwl/clt-step-values.yml";
+    /// use zefiro_cwl_parser::values::document::CwlValues;
+    /// let yaml_file = "test_data/cwl/clt-step-values.yml";
     /// let values = CwlValues::from_path(yaml_file).expect("Failed to deserialize CWL values document");
     /// ```
     pub fn from_path(path: &str) -> Result<Self, Error> {
@@ -49,7 +49,7 @@ impl CwlValues {
     /// Deserializes YAML `string` containing CWL values into CwlValues structure.
     ///
     /// ```
-    /// use zefiro_core_cwl::values::document::CwlValues;
+    /// use zefiro_cwl_parser::values::document::CwlValues;
     ///
     /// let yaml_input = r#"
     /// in_file:
@@ -78,7 +78,7 @@ impl CwlValues {
     /// Serializes CwlValues structure and writes it into `file`.
     ///
     /// ```
-    /// use zefiro_core_cwl::values::document::CwlValues;
+    /// use zefiro_cwl_parser::values::document::CwlValues;
     /// use std::io::BufWriter;
     ///
     /// let yaml_input = r#"
@@ -109,13 +109,13 @@ mod tests {
     use std::io::BufWriter;
 
     #[rstest]
-    #[case("examples/cwl/clt-step-values.yml")]
+    #[case("test_data/cwl/clt-step-values.yml")]
     fn test_cwlvalues_from_path(#[case] file_path: &str) {
         CwlValues::from_path(file_path).expect("Failed to deserialize CWL values document");
     }
 
     #[rstest]
-    #[case("examples/cwl/clt-step-values.yml")]
+    #[case("test_data/cwl/clt-step-values.yml")]
     fn test_cwlvalues_to_yaml(#[case] file_path: &str) {
         let values = CwlValues::from_path(file_path).expect("Failed to deserialize CWL values");
         let temp_file = tempfile::NamedTempFile::new().unwrap();

zefiro-pipeline/zefiro-cwl-parser/test_data/cwl/clt-step-values.yml

@@ -0,0 +1,4 @@
+in_file:
+  class: File
+  location: 'test_data/inputs/file.txt'
+out_file: 'test_data/inputs/output.txt'