create-academic-research 0.1.0 → 0.1.2

package/README.md

@@ -14,6 +14,9 @@ Equivalent explicit form:
 npx create-academic-research@latest my-project
 ```
 
+Prefer the explicit `@latest` form. Some npm/npx versions reuse an older
+cached creator when the version is omitted.
+
 From GitHub:
 
 ```bash
@@ -41,7 +44,7 @@ specific target recognized by the `skills` CLI, such as `claude-code`,
 By default, the wizard:
 
 - creates the repository structure;
-- configures project-local skills;
+- installs the project-local `VincenzoImp/academic-research-skills` package;
 - enables the scholarly MCP records for `arxiv`, `semantic-scholar`, and
   `openalex`;
 - writes `configs/capabilities.yaml`;
@@ -50,6 +53,10 @@ By default, the wizard:
 - appends the onboarding event to `wiki/log.md`;
 - does not install external MCP tools unless explicitly requested.
 
+Use `--preset enhanced` when you also want the curated complementary external
+skill bundles for agent engineering, frontend work, testing, document formats,
+and PDF conversion.
+
 ## Non-Interactive Create
 
 ```bash
@@ -71,6 +78,7 @@ npx academic-research doctor
 npx academic-research rename --title "New Title" --slug new-title --package new_title
 npx academic-research skills presets
 npx academic-research skills install --preset default
+npx academic-research skills install --preset enhanced
 npx academic-research skills list
 npx academic-research skills status
 npx academic-research skills remove source-ingestion
@@ -107,10 +115,10 @@ MCP commands are split by side-effect:
 | `mcp list` | List known MCP servers with enabled/available status. |
 | `mcp enabled` | List only enabled MCP server ids. |
 | `mcp available` | List the local MCP catalog. |
-| `mcp commands` | Print external install commands without running them. |
+| `mcp commands` | Print finite external install commands without running them. Runtime-only `uvx`/`npx` servers may have no install command. |
 | `mcp enable` | Enable an MCP server in project records and generated snippets. |
 | `mcp disable` | Remove an MCP server from project records and generated snippets. |
-| `mcp install` | Run the external tool install command for selected MCP servers. |
+| `mcp install` | Run finite external tool install commands for selected MCP servers. It must not launch stdio MCP servers. |
 | `mcp uninstall` | Run the external uninstall command when one exists. |
 | `mcp doctor` | Validate enabled MCP records and generated snippets. |
 
@@ -129,6 +137,17 @@ context. They are not automatic capabilities of every raw model API.
 Use `--agent <agent>` for explicit multi-tool setup; reserve `--agent '*'` for
 cases where you intentionally want every local agent loader populated.
 
+Preset intent:
+
+| Preset | Intent |
+|---|---|
+| `minimal` | Academic research skills only, no MCP records. |
+| `default` | Academic research skills plus core scholarly MCP records. |
+| `enhanced` | `default` plus curated external complementary skill bundles. |
+| `literature` | SOTA and systematic-review work with citation-library MCP records. |
+| `writing` | Paper-writing and Overleaf-oriented work. |
+| `full` | Broad optional connector and specialist setup. |
+
 ## Validate This Package
 
 ```bash
@@ -145,8 +164,8 @@ 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 v0.1.0 -m "v0.1.0"
-git push origin main v0.1.0
+git tag -a v0.1.2 -m "v0.1.2"
+git push origin main v0.1.2
 ```
 
 Once the GitHub repository is public, the release workflow validates the tag

package/dist/src/cli.js

@@ -36,7 +36,7 @@ async function createMain(argv) {
         return 0;
     }
     if (!target) {
-        printCreateHelp();
+        printMissingTargetHelp();
         return 1;
     }
     if (flagBool(parsed.flags, "install-skills") && flagBool(parsed.flags, "no-install-skills")) {
@@ -224,7 +224,7 @@ async function mcpCommand(argv) {
         const enabled = new Set(state.mcp_servers ?? []);
         for (const [name, server] of Object.entries(AGENT_STACK.mcp_servers)) {
             const status = enabled.has(name) ? "enabled" : "available";
-            const installer = server.install_command || "manual";
+            const installer = mcpInstallMode(server.install_command, server.command);
             console.log(`${status}\t${name}\t${server.source_need}\t${installer}`);
         }
         return 0;
@@ -242,7 +242,7 @@ async function mcpCommand(argv) {
         assertOnlyOptions(parsed.flags, "mcp available", []);
         assertNoArguments(parsed.positionals, "mcp available");
         for (const [name, server] of Object.entries(AGENT_STACK.mcp_servers)) {
-            const installer = server.install_command || "manual";
+            const installer = mcpInstallMode(server.install_command, server.command);
             console.log(`${name}\t${server.source_need}\t${installer}`);
         }
         return 0;
@@ -383,6 +383,11 @@ function assertOnlyOptions(flags, command, allowedOptions) {
         throw new Error(`${command} does not accept ${unexpected.map((name) => `--${name}`).join(", ")}`);
     }
 }
+function mcpInstallMode(installCommand, runtimeCommand) {
+    if (installCommand)
+        return installCommand;
+    return runtimeCommand ? "runtime-only" : "manual";
+}
 function printCreateHelp() {
     console.log([
         "Usage: create-academic-research <project-name> [options]",
@@ -394,16 +399,25 @@ function printCreateHelp() {
         "  --title <name>           Project title. Default: title-cased project name.",
         "  --slug <name>            Repository/package slug. Default: normalized project name.",
         "  --package <name>         Python package name. Default: normalized project name.",
-        "  --preset <name>           Capability preset: minimal, default, literature, writing, full.",
+        "  --preset <name>           Capability preset: minimal, default, enhanced, literature, writing, full.",
         "  --profile <name>          Project profile metadata. Default: academic-general.",
         "  --agent <name>            Agent target. Default: auto-detect.",
         "  --install-skills          Install project-local skills without prompting.",
         "  --no-install-skills       Skip project-local skill installation.",
-        "  --install-mcp-tools       Run external MCP install commands after creation.",
+        "  --install-mcp-tools       Run finite external MCP install commands after creation.",
         "  -h, --help               Show this help.",
         "  -v, --version            Show package version."
     ].join("\n"));
 }
+function printMissingTargetHelp() {
+    console.error([
+        "Please specify the project directory.",
+        "",
+        "Usage:",
+        "  npm create academic-research@latest my-research-project",
+        "  npx create-academic-research@latest my-research-project"
+    ].join("\n"));
+}
 function printLifecycleHelp() {
     console.log([
         "Usage: academic-research <doctor|rename|skills|mcp>",
@@ -432,7 +446,7 @@ function printMcpHelp() {
     console.log([
         "Usage: academic-research mcp <list|enabled|available|commands|enable|disable|install|uninstall|doctor> [servers...]",
         "",
-        "Manage MCP records and explicit external MCP tool installs.",
+        "Manage MCP records and finite external MCP tool installs.",
         "",
         "Options:",
         "  --root <path>            Project root for project-state commands.",

package/dist/src/project.js

@@ -205,7 +205,7 @@ 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 ?? "^0.1.0";
+    const packageSpec = process.env.CREATE_ACADEMIC_RESEARCH_PACKAGE_SPEC ?? existingSpec ?? "^0.1.2";
     data.name = slug;
     data.devDependencies = {
         ...(data.devDependencies ?? {}),

package/dist/src/stack.js

@@ -56,12 +56,17 @@ export const AGENT_STACK = {
     },
     presets: {
         minimal: {
-            description: "Only the academic research skill package.",
+            description: "Academic research skills only, no MCP records.",
             skill_bundles: ["academic_research"],
             mcp_servers: []
         },
         default: {
-            description: "Recommended setup for most academic research projects.",
+            description: "Clean academic research setup with core scholarly MCP records.",
+            skill_bundles: ["academic_research"],
+            mcp_servers: ["arxiv", "semantic-scholar", "openalex"]
+        },
+        enhanced: {
+            description: "Default academic setup plus complementary agent engineering, document, frontend, testing, and doc conversion skills.",
             skill_bundles: ["academic_research", "default_complementary", "docling"],
             mcp_servers: ["arxiv", "semantic-scholar", "openalex"]
         },
@@ -107,7 +112,7 @@ export const AGENT_STACK = {
         "semantic-scholar": {
             priority: "default",
             source_need: "Semantic Scholar papers, citations, authors, and recommendations.",
-            install_command: "uvx --from git+https://github.com/akapet00/semantic-scholar-mcp semantic-scholar-mcp --help",
+            install_command: "",
             uninstall_command: "",
             command: "uvx",
             args: ["--from", "git+https://github.com/akapet00/semantic-scholar-mcp", "semantic-scholar-mcp"],
@@ -118,7 +123,7 @@ export const AGENT_STACK = {
         openalex: {
             priority: "default",
             source_need: "OpenAlex broad scholarly graph.",
-            install_command: "npx -y @cyanheads/openalex-mcp-server --help",
+            install_command: "",
             uninstall_command: "",
             command: "npx",
             args: ["-y", "@cyanheads/openalex-mcp-server"],
@@ -140,7 +145,7 @@ export const AGENT_STACK = {
         pubmed: {
             priority: "domain-specific",
             source_need: "PubMed and biomedical literature.",
-            install_command: "npx -y @cyanheads/pubmed-mcp-server --help",
+            install_command: "",
             uninstall_command: "",
             command: "npx",
             args: ["-y", "@cyanheads/pubmed-mcp-server"],
@@ -151,7 +156,7 @@ export const AGENT_STACK = {
         zotero: {
             priority: "local-library",
             source_need: "Zotero local library and attachments.",
-            install_command: "uvx zoty --help",
+            install_command: "",
             uninstall_command: "",
             command: "uvx",
             args: ["zoty", "mcp"],

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "create-academic-research",
-  "version": "0.1.0",
+  "version": "0.1.2",
   "description": "Create and manage agent-ready academic research repositories.",
   "type": "module",
   "license": "MIT",

package/template/README.md

@@ -53,6 +53,7 @@ Project-local skills and MCP records are managed with:
 ```bash
 npx academic-research skills presets
 npx academic-research skills install --preset default
+npx academic-research skills install --preset enhanced
 npx academic-research skills list
 npx academic-research skills status
 npx academic-research mcp enable arxiv semantic-scholar openalex
@@ -63,6 +64,11 @@ npx academic-research mcp install arxiv
 
 `skills list` reports installed project-local skills. `skills presets` reports
 available install presets. `mcp enable` changes project records. `mcp commands`
-prints external install commands without running them. `mcp install` runs
-external tool installation commands and should be used only after reviewing the
-selected MCP.
+prints finite external install commands without running them. `mcp install`
+runs only finite tool installation commands; runtime-only `uvx`/`npx` MCP
+servers may have no install step and are started later by the MCP client.
+
+`default` installs the companion academic research skill package and keeps the
+MCP records focused on core scholarly discovery. `enhanced` adds complementary
+external skills for agent engineering, frontend work, testing, document
+formats, and PDF conversion.

package/template/package.json

@@ -12,6 +12,6 @@
     "mcp:doctor": "academic-research mcp doctor"
   },
   "devDependencies": {
-    "create-academic-research": "^0.1.0"
+    "create-academic-research": "^0.1.2"
   }
 }