feat(smartem-workspace): config refactor, dev requirements, claude opt-in

.github/workflows/publish-smartem-workspace.yml

@@ -1,4 +1,4 @@
-name: Publish smartem-workspace to PyPI
+name: smartem-workspace CLI tool PyPI package
 
 on:
   push:

core/claude-code-config.json

@@ -0,0 +1,46 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "version": "1.0.0",
+  "description": "Claude Code integration configuration for SmartEM workspace",
+  "claudeConfig": {
+    "skills": [
+      { "name": "database-admin", "path": "claude-code/shared/skills/database-admin" },
+      { "name": "devops", "path": "claude-code/shared/skills/devops" },
+      { "name": "technical-writer", "path": "claude-code/shared/skills/technical-writer" },
+      { "name": "git", "path": "claude-code/shared/skills/git" },
+      { "name": "github", "path": "claude-code/shared/skills/github" },
+      { "name": "ascii-art", "path": "claude-code/shared/skills/ascii-art" },
+      { "name": "playwright-skill", "path": "claude-code/smartem-frontend/skills/playwright-skill" }
+    ],
+    "defaultPermissions": {
+      "allow": [
+        "Bash(git:*)",
+        "Bash(ls:*)",
+        "Bash(cat:*)",
+        "WebSearch",
+        "mcp__serena__*"
+      ]
+    }
+  },
+  "serenaConfig": {
+    "languages": ["typescript", "python"],
+    "encoding": "utf-8",
+    "ignoreAllFilesInGitignore": true,
+    "projectName": "smartem-workspace"
+  },
+  "mcpConfig": {
+    "serena": {
+      "command": "uvx",
+      "args": [
+        "--from",
+        "git+https://github.com/oraios/serena",
+        "serena",
+        "start-mcp-server",
+        "--context",
+        "ide-assistant",
+        "--project",
+        "${PWD}"
+      ]
+    }
+  }
+}

core/claude-code-config.ts

@@ -0,0 +1,50 @@
+/**
+ * Claude Code integration configuration for SmartEM workspace.
+ *
+ * Source of truth: claude-code-config.json
+ * This file re-exports the JSON data with TypeScript types for type safety.
+ */
+
+import claudeCodeConfig from './claude-code-config.json'
+
+export interface SkillDefinition {
+  name: string
+  path: string
+}
+
+export interface DefaultPermissions {
+  allow: string[]
+}
+
+export interface ClaudeConfig {
+  skills: SkillDefinition[]
+  defaultPermissions: DefaultPermissions
+}
+
+export interface SerenaConfig {
+  languages: string[]
+  encoding: string
+  ignoreAllFilesInGitignore: boolean
+  projectName: string
+}
+
+export interface McpServerConfig {
+  command: string
+  args: string[]
+}
+
+export interface McpConfig {
+  serena: McpServerConfig
+}
+
+export interface ClaudeCodeConfigFile {
+  version: string
+  description: string
+  claudeConfig: ClaudeConfig
+  serenaConfig: SerenaConfig
+  mcpConfig: McpConfig
+}
+
+export const claudeCodeConfigData: ClaudeCodeConfigFile = claudeCodeConfig
+
+export default claudeCodeConfigData

core/dev-requirements.json

@@ -0,0 +1,79 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "version": "1.0.0",
+  "description": "Developer requirements for SmartEM workspace local environment setup",
+  "tools": [
+    {
+      "name": "git",
+      "command": "git",
+      "versionArgs": ["--version"],
+      "required": true,
+      "description": "Version control system"
+    },
+    {
+      "name": "Python",
+      "command": "python3",
+      "versionArgs": ["--version"],
+      "required": true,
+      "minVersion": "3.11",
+      "description": "Python interpreter (3.11+ required)"
+    },
+    {
+      "name": "uv",
+      "command": "uv",
+      "versionArgs": ["--version"],
+      "required": false,
+      "description": "Fast Python package installer (recommended)"
+    },
+    {
+      "name": "Node.js",
+      "command": "node",
+      "versionArgs": ["--version"],
+      "required": false,
+      "minVersion": "22",
+      "description": "JavaScript runtime for frontend development"
+    },
+    {
+      "name": "npm",
+      "command": "npm",
+      "versionArgs": ["--version"],
+      "required": false,
+      "description": "Node package manager"
+    },
+    {
+      "name": "Container runtime",
+      "command": "docker",
+      "versionArgs": ["--version"],
+      "required": false,
+      "alternatives": ["podman"],
+      "description": "Container runtime (docker or podman)"
+    },
+    {
+      "name": "kubectl",
+      "command": "kubectl",
+      "versionArgs": ["version", "--client", "--output=yaml"],
+      "required": false,
+      "description": "Kubernetes CLI"
+    },
+    {
+      "name": "k3s",
+      "command": "k3s",
+      "versionArgs": ["--version"],
+      "required": false,
+      "description": "Lightweight Kubernetes distribution"
+    },
+    {
+      "name": "gh",
+      "command": "gh",
+      "versionArgs": ["--version"],
+      "required": false,
+      "description": "GitHub CLI"
+    }
+  ],
+  "network": {
+    "checkUrl": "https://github.com",
+    "timeout": 5,
+    "required": false,
+    "description": "Network connectivity to GitHub"
+  }
+}

core/dev-requirements.ts

@@ -0,0 +1,36 @@
+/**
+ * Developer requirements for SmartEM workspace local environment setup.
+ *
+ * Source of truth: dev-requirements.json
+ * This file re-exports the JSON data with TypeScript types for type safety.
+ */
+
+import devRequirementsConfig from './dev-requirements.json'
+
+export interface ToolRequirement {
+  name: string
+  command: string
+  versionArgs: string[]
+  required: boolean
+  minVersion?: string
+  alternatives?: string[]
+  description: string
+}
+
+export interface NetworkCheck {
+  checkUrl: string
+  timeout: number
+  required: boolean
+  description: string
+}
+
+export interface DevRequirementsConfig {
+  version: string
+  description: string
+  tools: ToolRequirement[]
+  network: NetworkCheck
+}
+
+export const devRequirements: DevRequirementsConfig = devRequirementsConfig
+
+export default devRequirements

core/repos.json

@@ -358,46 +358,5 @@
         }
       ]
     }
-  ],
-  "claudeConfig": {
-    "skills": [
-      { "name": "database-admin", "path": "claude-code/shared/skills/database-admin" },
-      { "name": "devops", "path": "claude-code/shared/skills/devops" },
-      { "name": "technical-writer", "path": "claude-code/shared/skills/technical-writer" },
-      { "name": "git", "path": "claude-code/shared/skills/git" },
-      { "name": "github", "path": "claude-code/shared/skills/github" },
-      { "name": "ascii-art", "path": "claude-code/shared/skills/ascii-art" },
-      { "name": "playwright-skill", "path": "claude-code/smartem-frontend/skills/playwright-skill" }
-    ],
-    "defaultPermissions": {
-      "allow": [
-        "Bash(git:*)",
-        "Bash(ls:*)",
-        "Bash(cat:*)",
-        "WebSearch",
-        "mcp__serena__*"
-      ]
-    }
-  },
-  "serenaConfig": {
-    "languages": ["typescript", "python"],
-    "encoding": "utf-8",
-    "ignoreAllFilesInGitignore": true,
-    "projectName": "smartem-workspace"
-  },
-  "mcpConfig": {
-    "serena": {
-      "command": "uvx",
-      "args": [
-        "--from",
-        "git+https://github.com/oraios/serena",
-        "serena",
-        "start-mcp-server",
-        "--context",
-        "ide-assistant",
-        "--project",
-        "${PWD}"
-      ]
-    }
-  }
+  ]
 }

packages/smartem-workspace/README.md

@@ -19,6 +19,13 @@ uv tool install smartem-workspace
 
 ## Usage
 
+### Global options
+
+```
+--no-color          Disable colored output
+--plain             Plain mode: no color, no interactive prompts
+```
+
 ### Initialize a new workspace
 
 ```bash
@@ -77,6 +84,9 @@ Sync skips repos with uncommitted changes or not on main/master branch.
 # Show workspace status (alias for check)
 smartem-workspace status
 
+# Set up Claude Code integration (after init without --with-claude)
+smartem-workspace claude setup
+
 # Add a single repo (not yet implemented)
 smartem-workspace add DiamondLightSource/smartem-frontend
 ```
@@ -87,15 +97,19 @@ smartem-workspace add DiamondLightSource/smartem-frontend
 --path PATH         Target directory (default: current directory)
 --preset NAME       Use preset: smartem-core, full, aria-reference, minimal
 --no-interactive    Skip prompts, use preset only
---ssh               Use SSH URLs (default: HTTPS)
---skip-claude       Skip Claude Code setup
+--git-ssh           Force SSH URLs for all repos
+--git-https         Force HTTPS URLs (skip auto-detection)
+--with-claude       Enable Claude Code integration setup
 --skip-serena       Skip Serena MCP setup
+--skip-dev-requirements  Skip developer requirements check
 ```
 
+**Git URL auto-detection:** By default, the CLI automatically detects if you have SSH authentication configured for GitHub. If SSH works, repos are cloned via SSH (enabling push); otherwise HTTPS is used (read-only). Use `--git-ssh` or `--git-https` to override.
+
 ### Check options
 
 ```
---scope SCOPE       Check scope: claude, repos, serena, or all (default: all)
+--scope SCOPE       Check scope: dev-requirements, claude, repos, serena, or all (default: all)
 --fix               Attempt to fix issues (recreate symlinks, dirs)
 --offline           Use bundled config instead of fetching from GitHub
 ```
@@ -109,9 +123,9 @@ smartem-workspace add DiamondLightSource/smartem-frontend
 ## What it sets up
 
 1. **Repository clones** - Organized by organization (DiamondLightSource, FragmentScreen, GitlabAriaPHP)
-2. **Claude Code configuration** - Skills, settings, permissions
+2. **Claude Code configuration** (with `--with-claude`) - Skills, settings, permissions
 3. **Serena MCP server** - Semantic code navigation
-4. **Workspace structure** - CLAUDE.md, tmp/, testdata/ directories
+4. **Workspace structure** - tmp/, testdata/ directories
 
 ## Documentation