create-academic-research 0.1.7 → 0.1.8

package/README.md

@@ -93,6 +93,7 @@ npx academic-research agents list
 npx academic-research skills presets
 npx academic-research skills install --preset default
 npx academic-research skills install --preset enhanced
+npx academic-research skills install source-ingestion sota-literature-review
 npx academic-research skills list
 npx academic-research skills status
 npx academic-research skills remove source-ingestion
@@ -122,7 +123,7 @@ Skills are project-local by default.
 | Command | Meaning |
 |---|---|
 | `skills presets` | List available capability presets. |
-| `skills install` | Install project-local skills for the selected preset and project agent. This does not change MCP records. |
+| `skills install` | Install project-local skills by preset, or selected skill ids such as `source-ingestion`. This does not change MCP records. |
 | `skills list` | List skills found in project-local skill loader directories. |
 | `skills status` | Show configured project preset, agent, scope, skill roots, unique skill ids, and installed copies. |
 | `skills remove` / `skills uninstall` | Remove selected project-local skills. |
@@ -215,8 +216,8 @@ Releases are tag-driven. Update `package.json` and `package-lock.json`, commit
 the change, create `vX.Y.Z`, and push the tag:
 
 ```bash
-git tag -a v0.1.7 -m "v0.1.7"
-git push origin main v0.1.7
+git tag -a v0.1.8 -m "v0.1.8"
+git push origin main v0.1.8
 ```
 
 Once the GitHub repository is public, the release workflow validates the tag

package/dist/src/capabilities.d.ts

@@ -16,6 +16,7 @@ export interface InitializeCapabilitiesOptions {
 export interface CapabilityCommandResult {
     ok: true;
     count?: number;
+    skills?: string[];
     servers?: string[];
 }
 export interface InstalledSkill {
@@ -36,7 +37,9 @@ export declare function readCapabilities(root: string): Promise<CapabilityState>
 export declare function writeCapabilities(root: string, state: Partial<CapabilityState>): Promise<void>;
 export declare function initializeCapabilities(root: string, options?: InitializeCapabilitiesOptions): Promise<void>;
 export declare function buildSkillInstallCommands(root: string, preset?: string, options?: SkillInstallOptions): Promise<string[][]>;
+export declare function buildExplicitSkillInstallCommands(root: string, skills: string[], options?: SkillInstallOptions): Promise<string[][]>;
 export declare function installSkills(root: string, preset?: string, options?: SkillInstallOptions, runner?: Runner): Promise<CapabilityCommandResult>;
+export declare function installSkillIds(root: string, skills: string[], options?: SkillInstallOptions, runner?: Runner): Promise<CapabilityCommandResult>;
 export declare function listInstalledSkills(root: string): Promise<InstalledSkill[]>;
 export declare function removeSkills(root: string, skills: string[], runner?: Runner): Promise<CapabilityCommandResult>;
 export declare function updateSkills(root: string, runner?: Runner): Promise<CapabilityCommandResult>;

package/dist/src/capabilities.js

@@ -60,6 +60,21 @@ export async function buildSkillInstallCommands(root, preset = "default", option
     }
     return commands;
 }
+export async function buildExplicitSkillInstallCommands(root, skills, options = {}) {
+    const selectedSkills = normalizeSkillIds(skills);
+    const state = await readCapabilities(root);
+    const agent = assertKnownAgentTarget(options.agent ?? state.agent);
+    const skillsBySource = new Map();
+    for (const skill of selectedSkills) {
+        const source = skillSourceForId(skill);
+        if (!source)
+            throw new Error(`unknown skill id: ${skill}`);
+        const sourceSkills = skillsBySource.get(source) ?? [];
+        sourceSkills.push(skill);
+        skillsBySource.set(source, sourceSkills);
+    }
+    return [...skillsBySource.entries()].map(([source, sourceSkills]) => skillAddCommand(source, sourceSkills, agent));
+}
 export async function installSkills(root, preset = "default", options = {}, runner = defaultRunner) {
     const state = await readCapabilities(root);
     const agent = assertKnownAgentTarget(options.agent ?? state.agent);
@@ -76,6 +91,22 @@ export async function installSkills(root, preset = "default", options = {}, runn
     }
     return { ok: true, count: commands.length };
 }
+export async function installSkillIds(root, skills, options = {}, runner = defaultRunner) {
+    const state = await readCapabilities(root);
+    const agent = assertKnownAgentTarget(options.agent ?? state.agent);
+    const selectedSkills = normalizeSkillIds(skills);
+    const commands = await buildExplicitSkillInstallCommands(root, selectedSkills, options);
+    for (const command of commands) {
+        await runner.run(command, { cwd: root });
+    }
+    if (state.agent !== agent) {
+        await writeCapabilities(root, {
+            ...state,
+            agent
+        });
+    }
+    return { ok: true, count: commands.length, skills: selectedSkills };
+}
 export async function listInstalledSkills(root) {
     const roots = await discoverProjectSkillRoots(root);
     const skills = [];
@@ -287,6 +318,7 @@ async function writeCapabilityProfile(root, state) {
         "## Skills",
         "",
         `- Install with: \`academic-research skills install --preset ${state.preset ?? "default"}\``,
+        "- Install selected skills with: `academic-research skills install <skill-id> [...]`",
         "- List installed with: `academic-research skills list`",
         "- List presets with: `academic-research skills presets`",
         "- Remove with: `academic-research skills remove <skill>`",
@@ -355,6 +387,48 @@ function renderSkillCommand(command, agent) {
     const agentFlag = normalized === AUTO_AGENT ? "" : `--agent '${normalized}'`;
     return command.replaceAll("{agent_flag}", agentFlag).replaceAll("{agent}", normalized);
 }
+function skillAddCommand(source, skills, agent) {
+    return [
+        "npm",
+        "exec",
+        "--yes",
+        "--package",
+        "skills",
+        "--",
+        "skills",
+        "add",
+        source,
+        ...skillAgentArgs(agent),
+        "--skill",
+        ...skills,
+        "--copy",
+        "-y"
+    ];
+}
+function skillAgentArgs(agent) {
+    const normalized = assertKnownAgentTarget(agent);
+    return normalized === AUTO_AGENT ? [] : ["--agent", normalized];
+}
+function normalizeSkillIds(skills) {
+    if (skills.length === 0)
+        throw new Error("no skills selected");
+    const result = [];
+    for (const skill of skills) {
+        if (!/^[a-z0-9][a-z0-9._-]*$/.test(skill)) {
+            throw new Error(`invalid skill id: ${skill}`);
+        }
+        if (!result.includes(skill))
+            result.push(skill);
+    }
+    return result;
+}
+function skillSourceForId(skill) {
+    for (const source of Object.values(AGENT_STACK.skill_sources)) {
+        if (source.skills.includes(skill))
+            return source.source;
+    }
+    return undefined;
+}
 function appendMcpPrerequisiteLines(lines, requiredEnv, recommendedEnv, localService) {
     if (requiredEnv.length > 0)
         lines.push(`  - Requires env: ${requiredEnv.map((name) => `\`${name}\``).join(", ")}`);

package/dist/src/cli.js

@@ -1,7 +1,7 @@
 import { existsSync, readFileSync } from "node:fs";
 import { basename, delimiter, dirname, join, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
-import { assertKnownMcpServers, disableMcpServers, doctorMcpServers, enableMcpServers, DEFAULT_AGENT, installMcpTools, installSkills, listInstalledSkills, mcpToolCommandTexts, readCapabilities, removeSkills, uninstallMcpTools, updateSkills } from "./capabilities.js";
+import { assertKnownMcpServers, disableMcpServers, doctorMcpServers, enableMcpServers, DEFAULT_AGENT, installMcpTools, installSkillIds, installSkills, listInstalledSkills, mcpToolCommandTexts, readCapabilities, removeSkills, uninstallMcpTools, updateSkills } from "./capabilities.js";
 import { createProject, doctorProject, renameProject } from "./project.js";
 import { askCreateOptions } from "./prompts.js";
 import { AGENT_STACK, presetMcpServers } from "./stack.js";
@@ -9,7 +9,15 @@ import { formatAgentAliasLines, formatAgentTargetList, formatSupportedAgentTarge
 import { packageify, slugify, titleFromSlug } from "./names.js";
 const packageRoot = resolve(dirname(fileURLToPath(import.meta.url)), "../..");
 const packageVersion = readPackageVersion();
-const CREATE_FLAGS = flagSchema(["yes", "help", "version", "install-skills", "no-install-skills", "install-mcp-tools"], ["title", "slug", "package", "preset", "profile", "agent"]);
+const CREATE_FLAGS = flagSchema([
+    "yes",
+    "help",
+    "version",
+    "install-skills",
+    "no-install-skills",
+    "install-mcp-tools",
+    "no-install-mcp-tools"
+], ["title", "slug", "package", "preset", "profile", "agent"]);
 const ROOT_FLAGS = flagSchema(["help"], ["root"]);
 const RENAME_FLAGS = flagSchema(["help"], ["root", "title", "slug", "package"]);
 const SKILLS_FLAGS = flagSchema(["help"], ["root", "preset", "agent"]);
@@ -43,6 +51,9 @@ async function createMain(argv) {
     if (flagBool(parsed.flags, "install-skills") && flagBool(parsed.flags, "no-install-skills")) {
         throw new Error("cannot use --install-skills and --no-install-skills together");
     }
+    if (flagBool(parsed.flags, "install-mcp-tools") && flagBool(parsed.flags, "no-install-mcp-tools")) {
+        throw new Error("cannot use --install-mcp-tools and --no-install-mcp-tools together");
+    }
     if (parsed.positionals.length > 1) {
         throw new Error(`unexpected argument: ${parsed.positionals[1]}`);
     }
@@ -60,7 +71,9 @@ async function createMain(argv) {
     const installSkillsLock = flagBool(parsed.flags, "install-skills") || flagBool(parsed.flags, "no-install-skills")
         ? defaults.installSkills
         : undefined;
-    const installMcpToolsLock = flagBool(parsed.flags, "install-mcp-tools") ? true : undefined;
+    const installMcpToolsLock = flagBool(parsed.flags, "install-mcp-tools") || flagBool(parsed.flags, "no-install-mcp-tools")
+        ? defaults.installMcpTools
+        : undefined;
     const answers = interactive
         ? await askInteractiveCreateOptions(defaults, {
             installSkills: installSkillsLock,
@@ -240,8 +253,18 @@ async function skillsCommand(argv) {
     if (subcommand === "install") {
         assertOnlyOptions(parsed.flags, "skills install", ["root", "preset", "agent"]);
         const root = resolve(flagString(parsed.flags, "root") ?? ".");
-        assertNoArguments(parsed.positionals, "skills install");
-        const preset = flagString(parsed.flags, "preset") ?? "default";
+        const explicitSkills = parsed.positionals;
+        const explicitPreset = flagString(parsed.flags, "preset");
+        if (explicitSkills.length > 0) {
+            if (explicitPreset)
+                throw new Error("skills install does not accept --preset when skill ids are provided");
+            const result = await installSkillIds(root, explicitSkills, {
+                agent: flagString(parsed.flags, "agent")
+            });
+            console.log(`Installed ${result.skills?.length ?? explicitSkills.length} skill(s) with ${result.count ?? 0} command(s).`);
+            return 0;
+        }
+        const preset = explicitPreset ?? "default";
         const result = await installSkills(root, preset, {
             agent: flagString(parsed.flags, "agent")
         });
@@ -516,6 +539,7 @@ function printCreateHelp() {
         "  --install-skills          Install project-local skills without prompting.",
         "  --no-install-skills       Skip project-local skill installation.",
         "  --install-mcp-tools       Run finite external MCP install commands after creation.",
+        "  --no-install-mcp-tools    Skip finite external MCP install commands.",
         "  -h, --help               Show this help.",
         "  -v, --version            Show package version."
     ].join("\n"));
@@ -568,13 +592,17 @@ function printAgentsHelp() {
 }
 function printSkillsHelp() {
     console.log([
-        "Usage: academic-research skills <list|status|presets|install|remove|uninstall|update> [options]",
+        "Usage: academic-research skills <list|status|presets|install|remove|uninstall|update> [skill-id...] [options]",
         "",
         "Manage project-local skill installs for a generated research repository.",
         "",
+        "Examples:",
+        "  academic-research skills install --preset default",
+        "  academic-research skills install source-ingestion sota-literature-review",
+        "",
         "Options:",
         "  --root <path>            Project root for list, status, install, remove, uninstall, update.",
-        "  --preset <name>          Capability preset for install.",
+        "  --preset <name>          Capability preset for install when no skill ids are provided.",
         "  --agent <id>             Agent selector for install. Default: project capability agent.",
         "  -h, --help               Show this help."
     ].join("\n"));

package/dist/src/project.js

@@ -214,7 +214,7 @@ async function writeGeneratedPackageJson(root, { slug }) {
     const path = join(root, "package.json");
     const data = await readJson(path);
     const existingSpec = data.devDependencies?.["create-academic-research"];
-    const packageSpec = process.env.CREATE_ACADEMIC_RESEARCH_PACKAGE_SPEC ?? existingSpec ?? "0.1.7";
+    const packageSpec = process.env.CREATE_ACADEMIC_RESEARCH_PACKAGE_SPEC ?? existingSpec ?? "0.1.8";
     data.name = slug;
     data.devDependencies = {
         ...(data.devDependencies ?? {}),

package/dist/src/stack.d.ts

@@ -2,6 +2,11 @@ export interface SkillBundle {
     description: string;
     commands: string[];
 }
+export interface SkillSource {
+    description: string;
+    source: string;
+    skills: string[];
+}
 export interface CapabilityPreset {
     description: string;
     skill_bundles: string[];
@@ -30,6 +35,7 @@ export interface AgentStack {
     version: number;
     description: string;
     skill_bundles: Record<string, SkillBundle>;
+    skill_sources: Record<string, SkillSource>;
     presets: Record<string, CapabilityPreset>;
     mcp_servers: Record<string, McpServer>;
 }

package/dist/src/stack.js

@@ -22,6 +22,76 @@ export const AGENT_STACK = {
             ]
         }
     },
+    skill_sources: {
+        academic_research: {
+            description: "Academic research skills maintained by this project.",
+            source: "VincenzoImp/academic-research-skills",
+            skills: [
+                "academic-mcp-tooling",
+                "adversarial-peer-review",
+                "artifact-open-science",
+                "citation-bibliography-tooling",
+                "citation-claim-audit",
+                "cs-methodology-evaluation",
+                "cs-venue-strategy",
+                "document-conversion",
+                "ethics-data-governance",
+                "experiment-logbook",
+                "paper-writing-review",
+                "rebuttal-revision-strategy",
+                "repo-migration",
+                "research-data-analysis",
+                "research-design-positioning",
+                "research-project-maintenance",
+                "research-project-router",
+                "research-repo-reproduction",
+                "research-ui-prototyping",
+                "skill-evaluation",
+                "sota-literature-review",
+                "source-ingestion",
+                "systematic-review-prisma"
+            ]
+        },
+        superpowers: {
+            description: "General agent engineering skills from Superpowers.",
+            source: "obra/superpowers",
+            skills: [
+                "brainstorming",
+                "dispatching-parallel-agents",
+                "executing-plans",
+                "finishing-a-development-branch",
+                "receiving-code-review",
+                "requesting-code-review",
+                "subagent-driven-development",
+                "systematic-debugging",
+                "test-driven-development",
+                "using-git-worktrees",
+                "using-superpowers",
+                "verification-before-completion",
+                "writing-plans",
+                "writing-skills"
+            ]
+        },
+        anthropics: {
+            description: "Document, frontend, testing, MCP, and skill-authoring helpers.",
+            source: "anthropics/skills",
+            skills: [
+                "docx",
+                "frontend-design",
+                "mcp-builder",
+                "pdf",
+                "pptx",
+                "skill-creator",
+                "webapp-testing",
+                "xlsx"
+            ]
+        },
+        docling: {
+            description: "Document conversion helper from the Beagle collection.",
+            source: "existential-birds/beagle",
+            skills: ["docling"]
+        }
+    },
     presets: {
         minimal: {
             description: "Academic research skills only, no MCP records.",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "create-academic-research",
-  "version": "0.1.7",
+  "version": "0.1.8",
   "description": "Create and manage agent-ready academic research repositories.",
   "type": "module",
   "license": "MIT",

package/template/README.md

@@ -57,6 +57,7 @@ npx academic-research skills presets
 npx academic-research agents list
 npx academic-research skills install --preset default
 npx academic-research skills install --preset enhanced
+npx academic-research skills install source-ingestion sota-literature-review
 npx academic-research skills list
 npx academic-research skills status
 npx academic-research setup

package/template/package.json

@@ -15,6 +15,6 @@
     "mcp:doctor": "academic-research mcp doctor"
   },
   "devDependencies": {
-    "create-academic-research": "0.1.7"
+    "create-academic-research": "0.1.8"
   }
 }