snap to larger list of whitelisted R packages via views, bug fixes

Author: soodoku

.github/workflows/ci.yml

@@ -295,13 +295,26 @@ jobs:
         library(styler)
         files_to_check <- list.files(c('R', 'scripts'), pattern='[.]R\$', recursive=TRUE, full.names=TRUE)
         if (length(files_to_check) > 0) {
-          style_results <- styler::style_file(files_to_check, dry='on', include_roxygen_examples = FALSE)
-          if (any(style_results\$changed)) {
-            cat('❌ R code style issues found\\n')
+          cat('Checking style for', length(files_to_check), 'R files...\\n')
+          tryCatch({
+            style_results <- styler::style_file(files_to_check, dry='on', include_roxygen_examples = FALSE)
+            if (!is.null(style_results) && !any(is.na(style_results\$changed))) {
+              if (any(style_results\$changed)) {
+                cat('❌ R code style issues found\\n')
+                quit(status=1)
+              } else {
+                cat('✅ R code style check passed\\n')
+              }
+            } else {
+              cat('❌ R code style check encountered errors\\n')
+              quit(status=1)
+            }
+          }, error = function(e) {
+            cat('❌ R styling error:', e\$message, '\\n')
             quit(status=1)
-          } else {
-            cat('✅ R code style check passed\\n')
-          }
+          })
+        } else {
+          cat('✅ No R files found to check\\n')
         }
         "
     

CHANGELOG.md

@@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - JSON configuration file support (`~/.rmcp/config.json`, `/etc/rmcp/config.json`)
   - Command-line option overrides with `--config` and `--debug` flags
   - Type-safe configuration validation with detailed error messages
-  - Full documentation in `docs/configuration.md`
+  - Auto-generated documentation in `docs/configuration/` via Sphinx autodoc
 
 - **🔧 Enhanced CLI Interface**: Improved command-line experience
   - Global `--config` option to specify custom configuration files

README.md

@@ -6,7 +6,7 @@
 [![Documentation](https://github.com/finite-sample/rmcp/actions/workflows/docs.yml/badge.svg)](https://finite-sample.github.io/rmcp/)
 [![License](https://img.shields.io/github/license/finite-sample/rmcp)](https://github.com/finite-sample/rmcp/blob/main/LICENSE)
 
-**Turn conversations into comprehensive statistical analysis** - A Model Context Protocol (MCP) server with 44 statistical analysis tools across 11 categories. RMCP enables AI assistants to perform sophisticated statistical modeling, econometric analysis, machine learning, time series analysis, and data science tasks through natural conversation.
+**Turn conversations into comprehensive statistical analysis** - A Model Context Protocol (MCP) server with 44 statistical analysis tools across 11 categories and **429 R packages** from systematic CRAN task views. RMCP enables AI assistants to perform sophisticated statistical modeling, econometric analysis, machine learning, time series analysis, and data science tasks through natural conversation.
 
 ## 🚀 Quick Start (30 seconds)
 
@@ -77,17 +77,22 @@ Formula building, error recovery, example datasets → *"Help me build a regress
 
 ### Prerequisites
 - **Python 3.10+** 
-- **R 4.4.0+** with packages: Install all at once:
+- **R 4.4.0+** with **comprehensive package ecosystem**: RMCP uses a systematic 429-package whitelist from CRAN task views organized into 19+ categories:
 
 ```r
+# Core packages (install these first)
 install.packages(c(
-  "jsonlite", "plm", "lmtest", "sandwich", "AER", "dplyr",
-  "forecast", "vars", "urca", "tseries", "nortest", "car",
-  "rpart", "randomForest", "ggplot2", "gridExtra", "tidyr", 
-  "rlang", "knitr", "broom"
+  "jsonlite", "dplyr", "ggplot2", "broom", "plm", "forecast", 
+  "randomForest", "rpart", "caret", "AER", "vars", "mgcv"
 ))
+
+# Full ecosystem automatically available: Machine Learning (61 packages), 
+# Econometrics (55 packages), Time Series (48 packages), 
+# Bayesian Analysis (32 packages), and more
 ```
 
+**Package Selection**: Evidence-based using CRAN task views, download statistics, and 4-tier security assessment
+
 ### Install RMCP
 
 ```bash
@@ -165,17 +170,18 @@ rmcp start
 docker run -e RMCP_HTTP_HOST=0.0.0.0 -e RMCP_HTTP_PORT=8000 rmcp:latest
 ```
 
-**📖 [Complete Configuration Guide →](docs/configuration.md)**
+**📖 [Complete Configuration Guide →](docs/configuration/index.rst)** (auto-generated from code)
 
 ## 🔥 Key Features
 
 - **🎯 Natural Conversation**: Ask questions in plain English, get statistical analysis
+- **📚 Comprehensive Package Ecosystem**: 429 R packages from systematic CRAN task views with 4-tier security system
 - **📊 Professional Output**: Formatted results with markdown tables and inline visualizations  
 - **🔒 Production Ready**: Full MCP protocol compliance with HTTP transport and SSE
 - **⚙️ Flexible Configuration**: Environment variables, config files, and CLI options
 - **⚡ Fast & Reliable**: 100% test success rate across all scenarios
 - **🌐 Multiple Transports**: stdio (Claude Desktop) and HTTP (web applications)
-- **🛡️ Secure**: Controlled R execution with configurable permissions
+- **🛡️ Secure**: Evidence-based package selection with security-conscious permission tiers
 
 ## 📚 Documentation
 

docs/conf.py

@@ -21,17 +21,19 @@
     version = __version__
     release = __version__
 except ImportError:
-    version = "0.3.7"
-    release = "0.3.7"
+    version = "0.5.0"
+    release = "0.5.0"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
     "sphinx.ext.autodoc",
-    "sphinx.ext.autosummary",
+    "sphinx.ext.autosummary", 
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autosectionlabel",
     "myst_parser",
 ]
 
@@ -74,10 +76,16 @@
     "special-members": "__init__",
     "undoc-members": True,
     "exclude-members": "__weakref__",
+    "show-inheritance": True,
 }
+autodoc_typehints = "both"
+autodoc_typehints_description_target = "documented"
+autodoc_preserve_defaults = True
 
 # autosummary
 autosummary_generate = True
+autosummary_generate_overwrite = True
+autosummary_imported_members = False
 
 # napoleon - for Google/NumPy style docstrings
 napoleon_google_docstring = True
@@ -96,8 +104,13 @@
     "deflist",
     "tasklist",
     "colon_fence",
+    "attrs_inline",
+    "attrs_block", 
 ]
 
+# autosectionlabel 
+autosectionlabel_prefix_document = True
+
 # Copy button configuration
 copybutton_prompt_text = r">>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5,8}: "
 copybutton_prompt_is_regexp = True