create-academic-research 0.1.6 → 0.1.7

package/README.md

@@ -53,6 +53,9 @@ By default, the wizard:
 - writes `docs/agent/capability-profile.md`;
 - writes `docs/agent/mcp-setup.md`;
 - writes `docs/agent/generated/mcp.json` unless an explicit agent target is set;
+- includes `scripts/README.md` for repeatable command entrypoints;
+- includes reusable `wiki/templates/` pages for sources, claims, experiments,
+  decisions, reviewer concerns, and research questions;
 - appends the onboarding event to `wiki/log.md`;
 - does not install external MCP tools unless explicitly requested.
 
@@ -84,6 +87,7 @@ Inside a generated project:
 
 ```bash
 npx academic-research doctor
+npx academic-research setup
 npx academic-research rename --title "New Title" --slug new-title --package new_title
 npx academic-research agents list
 npx academic-research skills presets
@@ -99,15 +103,20 @@ npx academic-research mcp enabled
 npx academic-research mcp available
 npx academic-research mcp commands arxiv
 npx academic-research mcp env openalex semantic-scholar zotero
-npx academic-research mcp enable arxiv openalex
+npx academic-research mcp enable arxiv dblp
 npx academic-research mcp disable arxiv
 npx academic-research mcp install arxiv
 npx academic-research mcp uninstall arxiv
+npx academic-research mcp smoke
 npx academic-research mcp doctor
 ```
 
 ## Command Model
 
+`academic-research setup` is a non-destructive onboarding status command. It
+prints the active preset, agent, skill counts, enabled MCP records, and next
+commands without changing files.
+
 Skills are project-local by default.
 
 | Command | Meaning |
@@ -132,6 +141,7 @@ MCP commands are split by side-effect:
 | `mcp disable` | Remove an MCP server from project records and generated snippets. |
 | `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 smoke` | Print non-launching readiness diagnostics for enabled or selected MCP servers. |
 | `mcp doctor` | Validate enabled MCP records, generated snippets, required env vars, and documented manual prerequisites. |
 
 ## Companion Skills
@@ -185,6 +195,9 @@ live tools by themselves. Your MCP client must load the generated snippet, and
 the referenced commands must be available on your machine or runnable through
 `uvx`/`npx`. `mcp install` only runs finite setup commands such as the arXiv
 tool install; it deliberately does not launch stdio MCP servers.
+Use `mcp smoke` for a non-launching readiness pass before wiring a client: it
+checks required env vars, manual/local-service status, and whether runtime
+commands are visible on `PATH`.
 
 ## Validate This Package
 
@@ -202,8 +215,8 @@ 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 v0.1.6 -m "v0.1.6"
-git push origin main v0.1.6
+git tag -a v0.1.7 -m "v0.1.7"
+git push origin main v0.1.7
 ```
 
 Once the GitHub repository is public, the release workflow validates the tag

package/dist/src/cli.js

@@ -1,5 +1,5 @@
-import { readFileSync } from "node:fs";
-import { basename, dirname, join, resolve } from "node:path";
+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 { createProject, doctorProject, renameProject } from "./project.js";
@@ -100,6 +100,8 @@ async function lifecycleMain(argv) {
     }
     if (command === "doctor")
         return doctorCommand(argv.slice(1));
+    if (command === "setup")
+        return setupCommand(argv.slice(1));
     if (command === "rename")
         return renameCommand(argv.slice(1));
     if (command === "agents")
@@ -125,6 +127,41 @@ async function doctorCommand(argv) {
         console.log(`OK: ${root}`);
     return result.ok ? 0 : 1;
 }
+async function setupCommand(argv) {
+    const parsed = parseFlags(argv, ROOT_FLAGS);
+    if (flagBool(parsed.flags, "help")) {
+        printSetupHelp();
+        return 0;
+    }
+    assertNoArguments(parsed.positionals, "setup");
+    const root = resolve(flagString(parsed.flags, "root") ?? ".");
+    const project = await doctorProject(root);
+    const state = await readCapabilities(root);
+    const skills = await listInstalledSkills(root);
+    const skillIds = new Set(skills.map((skill) => skill.name));
+    console.log("Project Setup");
+    console.log(`root\t${root}`);
+    console.log(`doctor\t${project.ok ? "ok" : "error"}`);
+    console.log(`agent\t${state.agent}`);
+    console.log(`preset\t${state.preset}`);
+    console.log(`scope\t${state.scope}`);
+    console.log(`installed_skill_ids\t${skillIds.size}`);
+    console.log(`installed_skill_copies\t${skills.length}`);
+    console.log(`mcp_enabled\t${state.mcp_servers.length > 0 ? state.mcp_servers.join(",") : "none"}`);
+    if (!project.ok) {
+        for (const error of project.errors)
+            console.error(`ERROR: ${error}`);
+    }
+    console.log("");
+    console.log("Next Commands");
+    console.log(`academic-research skills install --preset ${state.preset}`);
+    console.log("academic-research skills status");
+    console.log("academic-research mcp list");
+    console.log("academic-research mcp env");
+    console.log("academic-research mcp smoke");
+    console.log("academic-research doctor");
+    return project.ok ? 0 : 1;
+}
 async function renameCommand(argv) {
     const parsed = parseFlags(argv, RENAME_FLAGS);
     if (flagBool(parsed.flags, "help")) {
@@ -317,6 +354,24 @@ async function mcpCommand(argv) {
         console.log(`Ran ${result.count ?? 0} MCP uninstall command(s).`);
         return 0;
     }
+    if (subcommand === "smoke") {
+        assertOnlyOptions(parsed.flags, "mcp smoke", ["root"]);
+        const root = resolve(flagString(parsed.flags, "root") ?? ".");
+        const state = await readCapabilities(root);
+        const explicitSelection = parsed.positionals.length > 0;
+        const selected = explicitSelection ? parsed.positionals : state.mcp_servers;
+        assertKnownMcpServers(selected);
+        const failed = printMcpSmokeDiagnostics(selected);
+        if (!explicitSelection) {
+            const result = await doctorMcpServers(root);
+            for (const error of result.errors)
+                console.error(`ERROR: ${error}`);
+            for (const warning of result.warnings)
+                console.warn(`WARN: ${warning}`);
+            return result.ok && !failed ? 0 : 1;
+        }
+        return failed ? 1 : 0;
+    }
     if (subcommand === "doctor") {
         assertOnlyOptions(parsed.flags, "mcp doctor", ["root"]);
         const root = resolve(flagString(parsed.flags, "root") ?? ".");
@@ -476,7 +531,7 @@ function printMissingTargetHelp() {
 }
 function printLifecycleHelp() {
     console.log([
-        "Usage: academic-research <doctor|rename|agents|skills|mcp>",
+        "Usage: academic-research <doctor|setup|rename|agents|skills|mcp>",
         "",
         "Manage a generated academic research repository after creation.",
         "",
@@ -485,6 +540,17 @@ function printLifecycleHelp() {
         "  -v, --version            Show package version."
     ].join("\n"));
 }
+function printSetupHelp() {
+    console.log([
+        "Usage: academic-research setup [options]",
+        "",
+        "Print project onboarding status and next commands without changing files.",
+        "",
+        "Options:",
+        "  --root <path>            Project root. Default: current directory.",
+        "  -h, --help               Show this help."
+    ].join("\n"));
+}
 function printAgentsHelp() {
     console.log([
         "Usage: academic-research agents <list>",
@@ -515,9 +581,9 @@ function printSkillsHelp() {
 }
 function printMcpHelp() {
     console.log([
-        "Usage: academic-research mcp <list|enabled|available|commands|env|enable|disable|install|uninstall|doctor> [servers...]",
+        "Usage: academic-research mcp <list|enabled|available|commands|env|enable|disable|install|uninstall|smoke|doctor> [servers...]",
         "",
-        "Manage MCP records and finite external MCP tool installs.",
+        "Manage MCP records, readiness checks, and finite external MCP tool installs.",
         "",
         "Options:",
         "  --root <path>            Project root for project-state commands.",
@@ -525,6 +591,32 @@ function printMcpHelp() {
         "  -h, --help               Show this help."
     ].join("\n"));
 }
+function printMcpSmokeDiagnostics(servers) {
+    let failed = false;
+    console.log("id\tstatus\truntime\tcheck");
+    for (const name of servers) {
+        const server = AGENT_STACK.mcp_servers[name];
+        const missingRequired = server.required_env.filter((envName) => !process.env[envName]);
+        if (missingRequired.length > 0)
+            failed = true;
+        const runtime = server.command ? [server.command, ...server.args].join(" ") : "manual setup";
+        let status = "manual";
+        if (missingRequired.length > 0) {
+            status = `missing-required-env:${missingRequired.join(",")}`;
+        }
+        else if (server.command && commandExists(server.command)) {
+            status = "runtime-found";
+        }
+        else if (server.command) {
+            status = "runtime-missing";
+        }
+        else if (server.local_service) {
+            status = "manual-local-service";
+        }
+        console.log(`${name}\t${status}\t${runtime}\t${server.smoke_test}`);
+    }
+    return failed;
+}
 function printMcpEnvironment(servers) {
     for (const name of servers) {
         const server = AGENT_STACK.mcp_servers[name];
@@ -553,6 +645,25 @@ function printMcpEnvironment(servers) {
             console.log(`${name}\tnone\t-`);
     }
 }
+function commandExists(command) {
+    if (!command)
+        return false;
+    if (command.includes("/") || command.includes("\\"))
+        return existsSync(command);
+    const pathValue = process.env.PATH ?? "";
+    const extensions = process.platform === "win32"
+        ? (process.env.PATHEXT ?? ".EXE;.CMD;.BAT;.COM").split(";")
+        : [""];
+    for (const directory of pathValue.split(delimiter).filter(Boolean)) {
+        for (const extension of extensions) {
+            const hasExtension = extension && command.toLowerCase().endsWith(extension.toLowerCase());
+            const candidate = join(directory, hasExtension ? command : `${command}${extension}`);
+            if (existsSync(candidate))
+                return true;
+        }
+    }
+    return false;
+}
 function readPackageVersion() {
     try {
         const packageJson = JSON.parse(readFileSync(join(packageRoot, "package.json"), "utf8"));

package/dist/src/project.js

@@ -138,10 +138,17 @@ export async function doctorProject(root) {
         "docs/agent/capability-profile.md",
         "docs/agent/mcp-setup.md",
         "docs/agent/generated",
+        "scripts/README.md",
         "sources/source-ledger.csv",
         "sota/literature-matrix.csv",
         "wiki/index.md",
-        "wiki/log.md"
+        "wiki/log.md",
+        "wiki/templates/source-page.md",
+        "wiki/templates/claim-page.md",
+        "wiki/templates/experiment-page.md",
+        "wiki/templates/decision-record.md",
+        "wiki/templates/reviewer-concern.md",
+        "wiki/templates/research-question.md"
     ];
     for (const relative of required) {
         if (!(await exists(join(target, relative))))
@@ -207,7 +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 ?? "0.1.6";
+    const packageSpec = process.env.CREATE_ACADEMIC_RESEARCH_PACKAGE_SPEC ?? existingSpec ?? "0.1.7";
     data.name = slug;
     data.devDependencies = {
         ...(data.devDependencies ?? {}),

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "create-academic-research",
-  "version": "0.1.6",
+  "version": "0.1.7",
   "description": "Create and manage agent-ready academic research repositories.",
   "type": "module",
   "license": "MIT",

package/template/AGENTS.md

@@ -6,7 +6,8 @@ scholarly record.
 ## Core Rules
 
 - Preserve source originals under `sources/`, `data/raw/`, and `data/external/`.
-- Keep reusable logic in `src/`; keep notebooks for exploration and narrative output.
+- Keep reusable logic in `src/`; keep `scripts/` as thin repeatable entrypoints.
+- Keep notebooks for exploration and narrative output.
 - Tie claims to sources, datasets, experiment records, or decision records.
 - Update durable records when project knowledge changes.
 - Keep large data, generated caches, credentials, and private review material out of git.
@@ -35,6 +36,8 @@ scholarly record.
 - `wiki/synthesis.md` changes only when the project-level interpretation changes.
 - `wiki/open_questions.md` tracks unresolved questions.
 - `wiki/contradictions.md` tracks conflicts across sources, data, or runs.
+- `wiki/templates/` contains reusable source, claim, experiment, decision,
+  reviewer-concern, and research-question page structures.
 
 ## Evidence
 
@@ -45,3 +48,4 @@ scholarly record.
 - Citation issues go in `sources/bib/citation-audit.csv`.
 - SOTA records go in `sota/`.
 - Curated experiment records go in `experiments/`.
+- Repeatable command entrypoints go in `scripts/`.

package/template/README.md

@@ -41,6 +41,7 @@ npx academic-research doctor
 - `docs/agent/`: active agent workflows, capability profile, and MCP setup.
 - `docs/methodology/`: research design, evaluation plan, and validity threats.
 - `experiments/`: curated experiment registry and run records.
+- `scripts/`: thin repeatable entrypoints that call reusable code in `src/`.
 - `notebooks/`: optional exploratory and narrative notebooks.
 - `outputs/`: final figures, tables, models, and paper-supporting derived assets.
 - `reports/`: proposal, paper, slides, reviews, and rebuttal material.
@@ -58,11 +59,13 @@ 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 setup
 npx academic-research mcp list
 npx academic-research mcp env openalex semantic-scholar zotero
 npx academic-research mcp enable arxiv dblp
 npx academic-research mcp commands arxiv
 npx academic-research mcp install arxiv
+npx academic-research mcp smoke
 npx academic-research mcp doctor
 ```
 
@@ -74,6 +77,12 @@ enable optional servers. `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.
 
+`setup` prints the current project capability state, installed skill counts,
+enabled MCP records, and the next onboarding commands without changing files.
+`mcp smoke` performs a non-launching MCP readiness check: it reports required
+env vars, local/manual setup, and whether client runtime commands such as `uvx`
+or `npx` are available.
+
 `default` installs the companion academic research skill package and keeps the
 MCP records focused on low-friction arXiv discovery. `literature` and `full`
 add DBLP for computer science bibliography. Credentialed, local-service, or

package/template/package.json

@@ -4,15 +4,17 @@
   "type": "module",
   "scripts": {
     "doctor": "academic-research doctor",
+    "setup": "academic-research setup",
     "skills:install": "academic-research skills install --preset default",
     "skills:list": "academic-research skills list",
     "skills:presets": "academic-research skills presets",
     "mcp:list": "academic-research mcp list",
     "mcp:commands": "academic-research mcp commands",
     "mcp:env": "academic-research mcp env",
+    "mcp:smoke": "academic-research mcp smoke",
     "mcp:doctor": "academic-research mcp doctor"
   },
   "devDependencies": {
-    "create-academic-research": "0.1.6"
+    "create-academic-research": "0.1.7"
   }
 }

package/template/scripts/README.md

@@ -0,0 +1,10 @@
+# Scripts
+
+Use this folder for thin, repeatable command entrypoints.
+
+Scripts should orchestrate project code, not contain core scientific logic. Put
+reusable methods, models, data transforms, and analysis functions in `src/`.
+
+Each script should make its inputs, outputs, config path, and expected side
+effects clear enough to reproduce later from `docs/reproducibility/` or an
+experiment record.

package/template/tests/test_project_structure.py

@@ -8,6 +8,7 @@ def test_core_research_structure_exists() -> None:
         "configs/default.yaml",
         "configs/capabilities.yaml",
         "docs/agent/capability-profile.md",
+        "scripts/README.md",
         "notebooks/README.md",
         "outputs/figures",
         "outputs/tables",
@@ -21,5 +22,11 @@ def test_core_research_structure_exists() -> None:
         "sota/literature-matrix.csv",
         "wiki/index.md",
         "wiki/log.md",
+        "wiki/templates/source-page.md",
+        "wiki/templates/claim-page.md",
+        "wiki/templates/experiment-page.md",
+        "wiki/templates/decision-record.md",
+        "wiki/templates/reviewer-concern.md",
+        "wiki/templates/research-question.md",
     ):
         assert (root / relative).exists()

package/template/wiki/index.md

@@ -7,3 +7,12 @@ This is the content index for the LLM-maintained project wiki.
 - [[synthesis]]
 - [[open_questions]]
 - [[contradictions]]
+
+## Templates
+
+- [[templates/source-page]]
+- [[templates/claim-page]]
+- [[templates/experiment-page]]
+- [[templates/decision-record]]
+- [[templates/reviewer-concern]]
+- [[templates/research-question]]

package/template/wiki/templates/claim-page.md

@@ -0,0 +1,24 @@
+# Claim: <claim_id>
+
+## Claim
+
+<fill: atomic claim>
+
+## Status
+
+- Verdict:
+- Confidence:
+- Last checked:
+
+## Evidence
+
+| source_or_run_id | path | support_span | verdict | notes |
+|---|---|---|---|---|
+
+## Safe Wording
+
+<fill: wording that current evidence supports>
+
+## Risk
+
+<fill: what would weaken, falsify, or narrow this claim>

package/template/wiki/templates/decision-record.md

@@ -0,0 +1,26 @@
+# Decision: <decision_id>
+
+## Context
+
+<fill: situation and constraints>
+
+## Decision
+
+<fill: chosen option>
+
+## Alternatives Considered
+
+| option | reason rejected |
+|---|---|
+
+## Evidence
+
+- Sources:
+- Experiments:
+- Reviews:
+
+## Consequences
+
+- Expected benefit:
+- Risk:
+- Review date:

package/template/wiki/templates/experiment-page.md

@@ -0,0 +1,30 @@
+# Experiment: <run_id>
+
+## Question
+
+<fill: research question or hypothesis>
+
+## Run
+
+- Date:
+- Git commit:
+- Command:
+- Config:
+- Seed:
+- Dataset:
+- Metric:
+- Output path:
+
+## Result
+
+<fill: measured outcome>
+
+## Interpretation
+
+<fill: claim status, limitations, and next action>
+
+## Links
+
+- Registry row: `experiments/registry.csv`
+- Related claims:
+- Related sources:

package/template/wiki/templates/research-question.md

@@ -0,0 +1,27 @@
+# Research Question: <rq_id>
+
+## Question
+
+<fill: answerable research question>
+
+## Scope
+
+- Population/domain:
+- Evidence type:
+- Exclusions:
+
+## Contribution Link
+
+- Candidate claim:
+- Closest prior work:
+- Delta:
+- Failure condition:
+
+## Evidence Plan
+
+| evidence_needed | path_or_source | status | risk |
+|---|---|---|---|
+
+## Current Status
+
+<fill: hypothesis, active, answered, rejected, or out of scope>

package/template/wiki/templates/reviewer-concern.md

@@ -0,0 +1,25 @@
+# Reviewer Concern: <concern_id>
+
+## Concern
+
+<fill: reviewer or internal-review concern>
+
+## Classification
+
+- Source:
+- Severity:
+- Paper location:
+- Claim or issue:
+- Action: concede | clarify | add-evidence | reframe | defend | defer
+
+## Evidence
+
+<fill: source, experiment, or manuscript evidence>
+
+## Response Plan
+
+<fill: exact response and manuscript change>
+
+## Status
+
+<fill: open, addressed, deferred, rejected with rationale>

package/template/wiki/templates/source-page.md

@@ -0,0 +1,31 @@
+# Source: <source_id>
+
+## Bibliographic Record
+
+- Title:
+- Authors:
+- Year:
+- Venue:
+- Identifiers:
+- Native path:
+- Derived path:
+- Metadata path:
+
+## Summary
+
+<fill: concise source summary>
+
+## Evidence Record
+
+- Supports:
+- Contradicts:
+- Method / data / metric:
+- Limitations:
+- Project relevance:
+- Claim strength:
+- Allowed wording:
+- Forbidden stronger wording:
+
+## Follow-Up
+
+- <fill: unresolved checks>