fix: build

Author: pesap

README.md

@@ -2,38 +2,6 @@
 
 A comprehensive framework plugin manager for the r2x power systems modeling ecosystem. Simplifies discovery, installation, and management of r2x framework plugins.
 
-## 🚧 Ongoing Refactoring TODO
-
-We're currently refactoring the plugin discovery and manifest system to be more dynamic and maintainable:
-
-### Completed ✅
-- [x] Simplified `DiscoveryPlugin` structure - no hardcoded fields, uses `constructor_args` + `resolved_references`
-- [x] Added dependency tracking to `Package` (`install_type`, `installed_by`, `dependencies`)
-- [x] Implemented AST parser Phase 1 - extracts all constructor args dynamically
-- [x] Implemented AST parser Phase 2 methods - resolves class/function references
-- [x] Refactored `AstDiscovery` - returns structs instead of JSON
-- [x] Reorganized manifest structure:
-  - `types.rs` - pure type definitions
-  - `manifest.rs` - all manifest operations (load, save, business logic)
-  - `manifest_writer.rs` - custom path utilities for testing
-- [x] Removed transitional `Plugin` struct
-
-### In Progress 🔄
-- [ ] Refactor `plugins/discovery.rs` to use new struct-based flow (no JSON parsing)
-- [ ] Implement AST parser Phase 3 - associate decorators with plugins
-- [ ] Update Python bridge (`plugin_invoker.rs`) to construct Python objects from `DiscoveryPlugin.constructor_args`
-- [ ] Update `commands/run.rs` to work directly with `DiscoveryPlugin`
-- [ ] Update `help.rs` to work directly with `DiscoveryPlugin`
-- [ ] Remove `plugin_parser.rs` (parse_plugin_json, parse_decorator_registrations) - no longer needed
-- [ ] Remove `plugin_manifest.rs` entirely
-- [ ] Update `plugin_cache.rs` to work with `DiscoveryPlugin`
-
-### Architecture Goals
-- **No intermediate representations**: Work directly with manifest data
-- **Python bridge constructs objects**: From `constructor_args` + `resolved_references`
-- **Manifest is source of truth**: No conversions, no hardcoded field assumptions
-- **Dependency tracking**: Proper cleanup when packages are removed
-
 ## Features
 
 - Easy plugin management
@@ -44,12 +12,6 @@ We're currently refactoring the plugin discovery and manifest system to be more
 
 This project uses [uv](https://github.com/astral-sh/uv) for handling Python packages. With uv, you don't need to worry about Python or plugin versioning—uv automatically handles dependency resolution and environment isolation for you.
 
-## License
-
-BSD-3-Clause License. See [LICENSE.txt](LICENSE.txt) for details.
-
-## Commands
-
 ### Getting Started
 
 ```bash
@@ -61,6 +23,7 @@ r2x init my-pipeline.yaml
 ```
 
 The `r2x init` command creates a template pipeline file with:
+
 - Example variables for substitution
 - Multiple pipeline examples
 - Plugin configuration templates
@@ -93,6 +56,7 @@ R2X_VENV_YES=1 r2x venv  # Skip confirmation with environment variable
 ```
 
 **Install packages in your managed venv:**
+
 ```bash
 uv pip install <package> --python $(r2x python path)
 ```
@@ -140,3 +104,7 @@ r2x read system.json
 # Load from stdin and open IPython with system available
 cat system.json | r2x read
 ```
+
+## License
+
+BSD-3-Clause License. See [LICENSE.txt](LICENSE.txt) for details.

crates/r2x-ast/Cargo.toml

@@ -16,11 +16,11 @@ publish = false
 anyhow = "1.0"
 ast-grep-core = "0.22"
 ast-grep-language = "0.22"
-r2x-manifest = { path = "../r2x-manifest" }
 tracing = "0.1"
 walkdir = "2.4"
 toml = { version = "0.9", features = ["preserve_order"] }
-r2x-logger = { path = "../r2x-logger" }
+r2x-manifest = {workspace=true}
+r2x-logger = {workspace=true}
 
 [dev-dependencies]
 tempfile = "3.10"

crates/r2x-cli/Cargo.toml

@@ -42,18 +42,23 @@ anyhow = "1.0"
 
 [dependencies.r2x-manifest]
 path = "../r2x-manifest"
+version = "0.0.1"
 
 [dependencies.r2x-ast]
 path = "../r2x-ast"
+version = "0.0.1"
 
 [dependencies.r2x-python]
 path = "../r2x-python"
+version = "0.0.1"
 
 [dependencies.r2x-config]
 path = "../r2x-config"
+version = "0.0.1"
 
 [dependencies.r2x-logger]
 path = "../r2x-logger"
+version = "0.0.1"
 
 [dev-dependencies]
 assert_cmd = "2.1"

crates/r2x-python/Cargo.toml

@@ -17,7 +17,8 @@ once_cell = "1.19"
 pyo3 = { version = "0.27", features = ["auto-initialize", "abi3-py38"] }
 serde_json = "1.0"
 tracing = "0.1"
-r2x-config = { path = "../r2x-config" }
-r2x-logger = { path = "../r2x-logger" }
-r2x-manifest = { path = "../r2x-manifest" }
 thiserror = "2.0"
+r2x-config = {workspace=true}
+r2x-logger = {workspace=true}
+r2x-manifest = {workspace=true}
+