Merge pull request #280 from fairagro/remove_init_arc

Init changes

Author: JensKrumsieck

CHANGELOG.md

@@ -2,6 +2,7 @@
 ## 🚀 Features
 - Updated the underlying CWL libraries to our [`commonwl`](https://github.com/fairagro/commonwl) library #236
 - Removed `annotate` command due to lack of usage
+- Removed `init` Option `-a` which could be used to create ARCs - from a long term perspective the ARC spec may change - if we are not able to provide updates everytime this feature obsoletes anyway
 
 ## 🐛 Bugfixes
 - ramping up runner conformance from 223/378 to 376/378

Cargo.lock

@@ -29,7 +29,8 @@ anyhow = "1.0.102"
 commonwl = { version = "0.8.1", features = ["engine"] }
 colored = "3.1.1"
 dialoguer = { version = "0.12.0", features = ["fuzzy-select"] }
-dircpy = "0.3.20"
+dircpy = "0.3.19"
+dunce = "1.0.5"
 fancy-regex = "0.18.0"
 git2 = { version = "0.21.0", features = ["vendored-openssl"] }
 keyring = { version = "3.6.3", features = [

Cargo.toml

@@ -157,26 +157,6 @@ Most commands need the context of a Git repo to work. Project initialization can
 ```bash
 s4n init -p <FOLDER/PROJECT NAME>
 ```
-Besides the minimal project structure, the creation of an ["Annotated Research Context"](https://arc-rdm.org/) or ARC is also possible.
-```bash
-s4n init -a -p <FOLDER/PROJECT NAME>
-```
-
-> [!IMPORTANT]
-> The commands have changed in v1.0.0 (**Breaking Change**). The mapping is as follows:
-> | Old Command               | New Command            |
->  |---------------------------|------------------------|
->  | s4n tool create           | s4n create             |
->  | s4n tool list             | s4n list               |
->  | s4n tool remove           | s4n remove             |
->  | s4n workflow create       | s4n create --name (optional!)|
->  | s4n workflow list         | s4n list               |
->  | s4n workflow remove       | s4n remove             |
->  | s4n workflow status       | s4n list [WORKFLOW_NAME]|
->  | s4n workflow connect      | s4n connect            |
->  | s4n workflow disconnect   | s4n disconnect         |
->  | s4n workflow visualize    | s4n visualize          |
->  | s4n workflow save         | s4n save               |
 
 ### Creation of CWL CommandLineTools
 To create [CWL](https://www.commonwl.org/) CommandLineTools which can be combined to workflows later a prefix command can be used. `s4n create` will execute any given command and creates a CWL CommandLineTool accordingly.

README.md

@@ -15,6 +15,5 @@ The `s4n init` command is used to initialize a SciWIn project. It will create a
 
     Options:
       -p, --project <PROJECT>  Name of the project
-      -a, --arc                Option to create basic arc folder structure
       -h, --help               Print help
     ```

docs/src/content/docs/reference/init.mdx

@@ -35,6 +35,8 @@ clap_complete = "4.5.61"
 ignore = "0.4.23"
 prettytable-rs = "0.10.0"
 
+dunce.workspace = true
+
 syntect = { version = "5.2.0", default-features = false, features = [
     "regex-fancy",
     "parsing",

packages/cli/Cargo.toml

@@ -1,27 +1,21 @@
 use anyhow::Context;
 use clap::Args;
 use log::info;
-use std::{env, path::PathBuf};
+use std::path::PathBuf;
 
 #[derive(Args, Debug, Default)]
 pub struct InitArgs {
     #[arg(short = 'p', long = "project", help = "Name of the project")]
     pub project: Option<String>,
-    #[arg(
-        short = 'a',
-        long = "arc",
-        help = "Option to create basic arc folder structure"
-    )]
-    pub arc: bool,
 }
 
 pub fn handle_init_command(args: &InitArgs) -> anyhow::Result<()> {
     let base_dir = match &args.project {
         Some(folder) => PathBuf::from(folder),
-        None => env::current_dir()?,
+        None => PathBuf::new(),
     };
 
-    s4n_core::project::initialize_project(&base_dir, args.arc)
+    s4n_core::project::initialize_project(&base_dir)
         .inspect_err(|_| {
             let _ = s4n_core::project::git_cleanup(args.project.clone());
         })
@@ -34,66 +28,36 @@ pub fn handle_init_command(args: &InitArgs) -> anyhow::Result<()> {
 mod tests {
     use super::*;
     use serial_test::serial;
+    use std::env;
     use tempfile::tempdir;
     use test_utils::check_git_user;
 
     #[test]
     #[serial]
-    fn test_init_s4n_without_folder_with_arc() {
-        //create a temp dir
+    fn test_init_s4n_without_folder() {
         let temp_dir = tempdir().expect("Failed to create a temporary directory");
+        let cwd = env::current_dir().unwrap();
+
         eprintln!("Temporary directory: {:?}", temp_dir.path());
         check_git_user().unwrap();
 
-        // Change current dir to the temporary directory to not create workflow folders etc in sciwin-client dir
         env::set_current_dir(temp_dir.path()).unwrap();
         eprintln!(
             "Current directory changed to: {}",
             env::current_dir().unwrap().display()
         );
 
-        // test method without folder name and do not create arc folders
         let folder_name: Option<String> = None;
-        let arc = true;
 
         let result = handle_init_command(&InitArgs {
             project: folder_name,
-            arc,
         });
 
-        // Assert results is ok and folders exist/ do not exist
         assert!(result.is_ok());
 
         assert!(PathBuf::from("workflows").exists());
         assert!(PathBuf::from(".git").exists());
-        assert!(PathBuf::from("assays").exists());
-        assert!(PathBuf::from("studies").exists());
-        assert!(PathBuf::from("runs").exists());
-    }
-
-    #[test]
-    #[serial]
-    fn test_init_s4n_with_arc() {
-        let temp_dir = tempdir().unwrap();
-        check_git_user().unwrap();
-        let arc = true;
-
-        let base_folder = Some(temp_dir.path().to_str().unwrap().to_string());
-
-        //call method with temp dir
-        let result = handle_init_command(&InitArgs {
-            project: base_folder,
-            arc,
-        });
-
-        assert!(result.is_ok(), "Expected successful initialization");
-
-        //check if directories were created
-        let expected_dirs = vec!["workflows", "assays", "studies", "runs"];
 
-        for dir in &expected_dirs {
-            let full_path = PathBuf::from(temp_dir.path()).join(dir);
-            assert!(full_path.exists(), "Directory {dir} does not exist");
-        }
+        env::set_current_dir(cwd).unwrap();
     }
 }

packages/cli/src/commands/init.rs

@@ -12,16 +12,17 @@ use test_utils::{check_git_user, setup_python};
 fn setup() -> (PathBuf, TempDir) {
     let dir = tempdir().unwrap();
 
-    //copy docs dit to tmp
+    //copy docs dir to tmp
     let test_folder = "../../testdata/docs";
     copy_dir(test_folder, dir.path()).unwrap();
 
     let current = env::current_dir().unwrap();
-    env::set_current_dir(dir.path()).unwrap();
+    let canonicalized = dunce::canonicalize(dir.path()).unwrap();
+    env::set_current_dir(&canonicalized).unwrap();
 
     //init
     check_git_user().unwrap();
-    initialize_project(dir.path(), false).expect("Could not init s4n");
+    initialize_project("").expect("Could not init s4n");
 
     (current, dir)
 }
@@ -499,7 +500,7 @@ pub async fn test_example_project() {
     check_git_user().unwrap();
 
     //init project
-    initialize_project(dir.path(), false).expect("Could not init s4n");
+    initialize_project("").expect("Could not init s4n");
 
     //create calculation tool
     create_tool(&CreateArgs {

packages/cli/tests/doc_tests.rs

@@ -47,7 +47,7 @@ pub fn test_remove_workflow() {
     let current = env::current_dir().unwrap();
     env::set_current_dir(dir.path()).unwrap();
 
-    initialize_project(dir.path(), false).unwrap();
+    initialize_project("").unwrap();
     create_workflow(&CreateArgs {
         name: Some("test".to_string()),
         ..Default::default()
@@ -78,7 +78,7 @@ pub fn test_workflow() -> Result<(), Box<dyn std::error::Error>> {
     let current = env::current_dir().unwrap();
 
     env::set_current_dir(dir.path()).unwrap();
-    initialize_project(dir.path(), false).unwrap();
+    initialize_project("").unwrap();
 
     create_and_write_file("workflows/calculation/calculation.cwl", CALCULATION_FILE).unwrap();
     create_and_write_file("workflows/plot/plot.cwl", PLOT_FILE).unwrap();
@@ -183,7 +183,7 @@ pub fn test_workflow_optional_flags() -> Result<(), Box<dyn std::error::Error>>
     let current = env::current_dir().unwrap();
 
     env::set_current_dir(dir.path()).unwrap();
-    initialize_project(dir.path(), false).unwrap();
+    initialize_project("").unwrap();
 
     create_and_write_file("workflows/calculation/calculation.cwl", CALCULATION_FILE).unwrap();
     create_and_write_file("workflows/plot/plot.cwl", PLOT_FILE).unwrap();

packages/cli/tests/workflow_integration_test.rs

@@ -25,12 +25,11 @@ semver = { version = "1.0.26", features = ["serde"] }
 shlex = "2.0.1"
 slugify = "0.1.0"
 smart-default = "0.7.1"
+dunce.workspace = true
 tokio.workspace = true
 tokio-util.workspace = true
 
 [dev-dependencies]
-calamine = "0.35.0"
-
 test_utils = { workspace = true }
 rstest = { workspace = true }
 serial_test = { workspace = true }