feat: package dependency <package-name> cmd to list dependencies

CLAUDE.md

@@ -3,7 +3,8 @@
 This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
 
 ## Project Overview
-This is a Go-based CLI tool for interacting with JuliaHub, a platform for Julia computing. The CLI provides commands for authentication, dataset management, registry management, project management, user information, token management, Git integration, and Julia integration.
+
+This is a Go-based CLI tool for interacting with JuliaHub, a platform for Julia computing. The CLI provides commands for authentication, dataset management, registry management, package management, project management, user information, token management, Git integration, and Julia integration.
 
 ## Architecture
 
@@ -13,7 +14,7 @@ The application follows a command-line interface pattern using the Cobra library
 - **auth.go**: OAuth2 device flow authentication with JWT token handling
 - **datasets.go**: Dataset operations (list, download, upload, status) with REST API integration
 - **registries.go**: Registry operations (list, config, add, update) with REST API integration
-- **packages.go**: Package search with REST API primary path (`/packages/info`) and GraphQL fallback
+- **packages.go**: Package operations (search, dependency) with REST API primary path (`/packages/info`), GraphQL fallback, and documentation API (`/docs/{registry}/{package}/stable/pkg.json`)
 - **projects.go**: Project management using GraphQL API with user filtering
 - **user.go**: User information retrieval using GraphQL API and REST API for listing users
 - **tokens.go**: Token management operations (list) with REST API integration
@@ -42,9 +43,8 @@ The application follows a command-line interface pattern using the Cobra library
    - `jh dataset`: Dataset operations (list, download, upload, status)
    - `jh registry`: Registry operations (list, config — all via REST API)
    - `jh registry config`: Show registry JSON config by name; subcommands add/update accept JSON via stdin or `--file`
-   - `jh package`: Package search and info (REST primary via `/packages/info`, GraphQL fallback; supports filtering by registry)
+   - `jh package`: Package search and dependency (REST primary via `/packages/info`, GraphQL fallback; dependency data from `/docs/{registry}/{package}/stable/pkg.json`)
    - `jh project`: Project management (list with GraphQL, supports user filtering)
-   - `jh package`: Package search (REST primary via `/packages/info`, GraphQL fallback)
    - `jh user`: User information (info with GraphQL)
    - `jh admin`: Administrative commands (user management, token management, landing page)
    - `jh admin user`: User management (list all users with REST API, supports verbose mode)
@@ -103,6 +103,12 @@ go run . package search --limit 20 ml
 go run . package search --registries General optimization
 go run . package info DataFrames
 go run . package info Plots --registries General
+
+# Get package dependencies
+go run . package dependency DataFrames
+go run . package dependency DataFrames --indirect
+go run . package dependency DataFrames --all --indirect
+go run . package dependency CSV --registry General
 ```
 
 ### Test registry operations
@@ -230,9 +236,11 @@ The application uses OAuth2 device flow:
 
 ### REST API Integration
 - **Dataset operations**: Use presigned URLs for upload/download
+- **Registry operations**: `/api/v1/registry/registries/descriptions` for listing registries
 - **User management**: `/app/config/features/manage` endpoint for listing all users
 - **Token management**: `/app/token/activelist` endpoint for listing all API tokens
-- **Package search primary**: `/packages/info` endpoint with `name`, `registries`, `tags`, `licenses`, `limit`, `offset` query params; returns `{packages: [...], meta: {total: N}}`
+- **Package search/info primary**: `/packages/info` endpoint with `name`, `registries`, `tags`, `licenses`, `limit`, `offset` query params; returns `{packages: [...], meta: {total: N}}`
+- **Package dependencies**: `/docs/{registry}/{package}/stable/pkg.json` for dependency information
 - **Authentication**: Bearer token with ID token
 - **Upload workflow**: 3-step process (request presigned URL, upload to URL, close upload)
 
@@ -286,6 +294,41 @@ git clone https://github.com/user/repo.git                          # Ignored by
 - **Token management**: Stores and refreshes tokens per server automatically
 - **Error handling**: Graceful fallback to other credential helpers for non-JuliaHub URLs
 
+## Package Management
+
+The CLI provides comprehensive package discovery and dependency analysis:
+
+### Package Search and Info
+- **Search**: `jh package search` uses GraphQL API to search packages across registries
+- **Info**: `jh package info` retrieves detailed package metadata
+- **Filtering**: Supports filtering by registry, installation status, and failures
+
+### Package Dependency (`jh package dependency`)
+- **Endpoint**: Uses package documentation API at `/docs/{registry}/{package}/stable/pkg.json`
+- **Registry resolution**: Automatically uses first registry package belongs to, or specific registry via `--registry` flag
+- **Dependency types**: Distinguishes between direct and indirect dependencies via `direct` field in API response
+- **Display limits**:
+  - Default: Shows up to 10 direct dependencies
+  - With `--indirect`: Shows up to 10 direct and 50 indirect dependencies
+  - With `--all`: Shows all dependencies without limits
+- **Output format**:
+  - Direct-only mode: Single table with columns: NAME, REGISTRY, UUID, VERSIONS
+  - Indirect mode: Separate sections for direct and indirect dependencies with columns: NAME, REGISTRY, UUID, VERSIONS
+  - Registry column shows which registry each dependency belongs to (empty for stdlib packages)
+
+#### Implementation Details (`packages.go`)
+- `getPackageDependencies()`: Main function for dependency retrieval
+  1. Fetches all registries to get registry IDs for GraphQL query
+  2. Searches for package using GraphQL to get registry information
+  3. Determines target registry (first registry or user-specified)
+  4. Fetches package documentation JSON from docs endpoint
+  5. Filters and limits dependencies based on flags
+  6. Displays results in formatted tables with separate sections
+
+#### Data Structures
+- `PackageDependency`: Represents a single dependency with fields for direct/indirect status, name, UUID, versions, registry, and slug
+- `PackageDocsResponse`: Response from documentation API containing package metadata and dependencies array
+
 ## Julia Integration
 
 The CLI provides Julia installation and execution with JuliaHub configuration:
@@ -362,14 +405,15 @@ jh run setup
 - Landing page commands (`jh admin landing-page`) use REST API: GET `/app/homepage` (show), POST `/app/config/homepage` (update), DELETE `/app/config/homepage` (remove); require appropriate permissions
 - Landing page `update` command accepts content inline as an argument, from a file via `--file`, or piped via stdin (priority: `--file` > arg > stdin)
 - Landing page response uses custom JSON unmarshaling (`homepageResponse`) to handle `message` being either an object or a string
-- Package search (`jh package search`) and info (`jh package info`) both try REST API (`/packages/info`) first, then fall back to GraphQL (`FilteredPackagesWithCount` via `/v1/graphql`) on failure; a warning is printed to stderr when the fallback is used
+- Package search (`jh package search`) and info (`jh package info`) both try REST API (`/packages/info`) first, then fall back to GraphQL (`FilteredPackages` / `FilteredPackagesCount` via `/v1/graphql`) on failure; a warning is printed to stderr when the fallback is used
 - REST API passes `--registries` as comma-separated registry names to the `registries` query param; GraphQL fallback passes registry IDs to the `registries` variable
-- `fetchRegistries` in `registries.go` is used by `listRegistries`, `packageSearchCmd`, and `packageInfoCmd` to resolve registry names to IDs (for GraphQL) and names (for REST)
+- `fetchRegistries` in `registries.go` is used by `listRegistries`, `packageSearchCmd`, `packageInfoCmd`, and `packageDependencyCmd` to resolve registry names to IDs (for GraphQL) and names (for REST)
 - Both REST and GraphQL package search/info paths produce identical output columns (Registry and Owner); GraphQL resolves registry names from the `registryIDs`/`registryNames` already in `PackageSearchParams` — no extra API call needed
 - A package in multiple registries appears as multiple rows (one per registry) in both REST and GraphQL paths, since the GraphQL view (`package_rank_vw`) is already flattened per package-registry combination
-- GraphQL fallback uses `package_search_with_count.gql` which fetches both the package list and aggregate count in a single request (`package_search` + `package_search_aggregate` root fields)
+- GraphQL fallback uses `package_search.gql` (`FilteredPackages`) for the package list and `package_search_count.gql` (`FilteredPackagesCount`) for the aggregate count as separate requests
 - `executeGraphQL(server, token, req)` in `packages.go` is a shared helper for GraphQL POST requests (sets Authorization, Content-Type, Accept, X-Hasura-Role headers)
 - `getPackageInfo` in `packages.go` implements exact name-match lookup using REST-first (`getPackageInfoREST`), GraphQL fallback (`getPackageInfoGraphQL`); `packageInfoCmd` in `main.go` resolves registries via `fetchRegistries`
+- `getPackageDependencies` uses GraphQL (`fetchGraphQLPackages`) to locate the package, then fetches `/docs/{registry}/{package}/stable/pkg.json` for dependency data; no REST fallback (docs endpoint is authoritative)
 
 ## Implementation Details
 

README.md

@@ -6,8 +6,13 @@ A command-line interface for interacting with JuliaHub, a platform for Julia com
 
 - **Authentication**: OAuth2 device flow authentication with JWT token handling
 - **Dataset Management**: List, download, upload, and check status of datasets
+<<<<<<< HEAD
+- **Package Management**: Search and explore Julia packages across registries via REST API (GraphQL fallback), with dependency analysis
+- **Registry Management**: List and manage Julia package registries
+=======
 - **Package Management**: Search and explore Julia packages across registries via REST API (GraphQL fallback)
 - **Registry Management**: List, add, and update Julia package registries
+>>>>>>> 4c422aed3b5e0e488e6e479143bd5bec64385463
 - **Project Management**: List and filter projects using GraphQL API
 - **Git Integration**: Clone, push, fetch, and pull with automatic JuliaHub authentication
 - **Julia Integration**: Install Julia and run with JuliaHub package server configuration
@@ -171,6 +176,13 @@ go build -o jh .
 - `jh registry config add` - Add a new registry (JSON payload via stdin or `--file`)
 - `jh registry config update` - Update an existing registry (same JSON schema as add, same flags)
 
+- `jh package dependency <package-name>` - List package dependencies
+  - Default: Shows up to 10 direct dependencies (NAME, REGISTRY, UUID, VERSIONS)
+  - `jh package dependency --indirect` - Include indirect dependencies (up to 10 direct, 50 indirect)
+  - `jh package dependency --all` - Show all dependencies without limits
+  - `jh package dependency --registry General` - Specify registry to use
+
+
 ### Project Management (`jh project`)
 
 - `jh project list` - List all accessible projects
@@ -274,6 +286,12 @@ jh package search --limit 20 --offset 0 ml
 # Get detailed info about a specific package
 jh package info DataFrames
 jh package info Plots --registries General
+
+# List package dependencies
+jh package dependency DataFrames              # Shows up to 10 direct dependencies
+jh package dependency DataFrames --indirect   # Includes indirect dependencies
+jh package dependency DataFrames --all --indirect  # Shows all dependencies
+jh package dependency CSV --registry General  # Use specific registry
 ```
 
 ### Registry Operations
@@ -419,7 +437,7 @@ Note: Arguments after `--` are passed directly to Julia. The `jh run` command:
 
 - **Built with Go** using the Cobra CLI framework
 - **Authentication**: OAuth2 device flow with JWT token management
-- **APIs**: REST API for datasets and package search/info (primary); GraphQL API for projects, user info, and package search/info fallback (single request returns results + total count)
+- **APIs**: REST API for datasets and package search/info (primary); GraphQL API for projects, user info, package search/info fallback, and package dependency lookup
 - **Git Integration**: Seamless authentication via HTTP headers or credential helper
 - **Cross-platform**: Supports Windows, macOS, and Linux
 

main.go

@@ -818,6 +818,38 @@ The package name must match exactly (case-insensitive).`,
 	},
 }
 
+var packageDependencyCmd = &cobra.Command{
+	Use:   "dependency <package-name>",
+	Short: "List package dependencies",
+	Long: `List dependencies for a specific Julia package.
+
+By default, shows all direct dependencies. Use --indirect flag to include
+both direct and indirect dependencies.
+
+The command fetches dependency information from the package documentation
+JSON endpoint. If a package exists in multiple registries, it uses the
+first registry by default. You can specify a different registry using
+the --registry flag.`,
+	Example: "  jh package dependency DataFrames\n  jh package dependency --indirect Plots\n  jh package dependency --registry General CSV",
+	Args:    cobra.ExactArgs(1),
+	Run: func(cmd *cobra.Command, args []string) {
+		server, err := getServerFromFlagOrConfig(cmd)
+		if err != nil {
+			fmt.Printf("Failed to get server config: %v\n", err)
+			os.Exit(1)
+		}
+
+		packageName := args[0]
+		registryName, _ := cmd.Flags().GetString("registry")
+		showIndirect, _ := cmd.Flags().GetBool("indirect")
+
+		if err := getPackageDependencies(server, packageName, registryName, showIndirect); err != nil {
+			fmt.Printf("Failed to get package dependencies: %v\n", err)
+			os.Exit(1)
+		}
+	},
+}
+
 var registryCmd = &cobra.Command{
 	Use:   "registry",
 	Short: "Registry management commands",
@@ -1618,6 +1650,9 @@ func init() {
 	packageSearchCmd.Flags().Bool("verbose", false, "Show detailed package information")
 	packageInfoCmd.Flags().StringP("server", "s", "juliahub.com", "JuliaHub server")
 	packageInfoCmd.Flags().String("registries", "", "Filter by registry names (comma-separated, e.g., 'General,CustomRegistry')")
+	packageDependencyCmd.Flags().StringP("server", "s", "juliahub.com", "JuliaHub server")
+	packageDependencyCmd.Flags().String("registry", "", "Specify registry name (uses first registry if not specified)")
+	packageDependencyCmd.Flags().Bool("indirect", false, "Include indirect dependencies")
 	registryListCmd.Flags().StringP("server", "s", "juliahub.com", "JuliaHub server")
 	registryListCmd.Flags().Bool("verbose", false, "Show detailed registry information")
 	projectListCmd.Flags().StringP("server", "s", "juliahub.com", "JuliaHub server")
@@ -1640,7 +1675,7 @@ func init() {
 	authCmd.AddCommand(authLoginCmd, authRefreshCmd, authStatusCmd, authEnvCmd)
 	jobCmd.AddCommand(jobListCmd, jobStartCmd)
 	datasetCmd.AddCommand(datasetListCmd, datasetDownloadCmd, datasetUploadCmd, datasetStatusCmd)
-	packageCmd.AddCommand(packageSearchCmd, packageInfoCmd)
+	packageCmd.AddCommand(packageSearchCmd, packageInfoCmd, packageDependencyCmd)
 	registryConfigCmd.Flags().StringP("server", "s", "", "JuliaHub server")
 	registryConfigAddCmd.Flags().StringP("server", "s", "juliahub.com", "JuliaHub server")
 	registryConfigAddCmd.Flags().StringP("file", "f", "", "Path to JSON config file (reads from stdin if omitted)")

package_search_count.gql

@@ -0,0 +1,27 @@
+query FilteredPackagesCounts(
+  $search: String
+  $matchtags: _text
+  $registries: _int8
+  $hasfailures: Boolean
+  $installed: Boolean
+  $notinstalled: Boolean
+  $licenses: _text
+  $filter: package_rank_vw_bool_exp = {}
+) {
+  package_search_aggregate(
+    args: {
+      search: $search
+      matchtags: $matchtags
+      licenses: $licenses
+      isinstalled: $installed
+      notinstalled: $notinstalled
+      hasfailures: $hasfailures
+      registrylist: $registries
+    }
+    where: { _and: [{ fit: { _gte: 1 } }, $filter] }
+  ) {
+    aggregate {
+      count
+    }
+  }
+}