nemar-cli 0.10.1-dev.2434 → 0.10.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/index.js +3 -3
- package/package.json +1 -1
package/dist/index.js
CHANGED
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@@ -99,18 +99,18 @@ ${t}`,qDe,jDe,MDe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,i=NDe.bind(nul
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`)}var lD=!1;var{spawn:b9e}=globalThis.Bun;async function A(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=b9e({cmd:e,cwd:t.cwd,stdout:"pipe",stderr:"pipe",env:r}),i=!1,o;if(t.timeout)o=setTimeout(()=>{i=!0,n.kill()},t.timeout);if(uD()){let u=t.cwd?` (cwd=${t.cwd})`:"";of(l.dim(`$ ${e.join(" ")}${u}`))}let s=await new Response(n.stdout).text(),a=await new Response(n.stderr).text(),c=await n.exited;if(o)clearTimeout(o);if(uD()){if(s.trim())of(l.dim(s.trimEnd()));if(a.trim())of(l.yellow(a.trimEnd()));of(l.dim(`(exit ${c})`))}if(i)return{stdout:s,stderr:a||`Command timed out after ${Math.round(t.timeout/1000)}s`,exitCode:c??1,timedOut:!0};return{stdout:s,stderr:a,exitCode:c,timedOut:!1}}var sr=O(()=>{Xe()});function v9e(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function jW(e,t=v9e()){return e.installInstructions[t]}function w9e(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function E9e(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:D9e}async function MW(e){try{let{exitCode:t,stdout:r,timedOut:n}=await A(e.cmd,{timeout:E9e()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:w9e(r)}}catch(t){let r=t instanceof Error?t.message:String(t);if(!r.includes("ENOENT")&&!r.includes("not found"))console.error(` Warning: ${e.name} check failed unexpectedly: ${r}`);return{available:!1}}}async function sf(){let e=Object.entries(qW);return Promise.all(e.map(async([t,r])=>{let{available:n,version:i,timedOut:o}=await MW(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:i,timedOut:o,installInstruction:jW(r)}}))}async function LW(){let t=(await sf()).filter((r)=>r.required&&!r.available);if(t.length===0)return[];console.warn(`
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Heads up: some tools NEMAR needs for uploading/validating aren't installed yet:`);for(let r of t)console.warn(` - ${r.name} (${r.purpose})`),console.warn(` Install: ${r.installInstruction}`);return console.warn("Run `nemar doctor` anytime to re-check. You can finish signup without them.\n"),t}async function sa(e){let r=_9e[e].map((s)=>qW[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await MW(s);return{check:s,available:a.available,timedOut:a.timedOut}}));for(let s of n)if(s.timedOut&&s.check.required)console.warn(`Warning: ${s.check.name} did not respond to a version check in time; continuing anyway.`);let i=n.filter((s)=>!s.available&&!s.timedOut&&s.check.required).map((s)=>({tool:s.check.name,installInstruction:jW(s.check)}));if(i.length===0)return;let o=[`
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Missing required tools:`];for(let s of i)o.push(` ${s.tool} not installed`),o.push(` Install: ${s.installInstruction}`);throw Error(o.join(`
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`))}var qW,_9e,D9e=4000;var af=O(()=>{sr();qW={git:{name:"git",purpose:"version control for dataset metadata",cmd:["git","--version"],required:!0,installInstructions:{macos:"brew install git (or install Xcode Command Line Tools)",linux:"sudo apt-get install git OR sudo dnf install git",windows:"winget install Git.Git (or https://git-scm.com/download/win)"}},"git-annex":{name:"git-annex",purpose:"large-file data transfer (upload/download)",cmd:["git-annex","version"],required:!0,installInstructions:{macos:"brew install git-annex",linux:"sudo apt-get install git-annex OR sudo dnf install git-annex",windows:"Download the installer from https://git-annex.branchable.com/install/Windows/"}},gh:{name:"GitHub CLI (gh)",purpose:"GitHub authentication + repository operations",cmd:["gh","--version"],required:!0,installInstructions:{macos:"brew install gh",linux:"See https://cli.github.com/manual/installation",windows:"winget install GitHub.cli (or: scoop install gh)"}},aws:{name:"AWS CLI",purpose:"S3 data upload/download",cmd:["aws","--version"],required:!0,installInstructions:{macos:"brew install awscli",linux:"pip install awscli OR sudo snap install aws-cli --classic",windows:"winget install Amazon.AWSCLI (or the MSI from https://aws.amazon.com/cli/)"}},deno:{name:"Deno",purpose:"BIDS validation",cmd:["deno","--version"],required:!0,installInstructions:{macos:"brew install deno (or: curl -fsSL https://deno.land/install.sh | sh)",linux:"curl -fsSL https://deno.land/install.sh | sh",windows:"winget install DenoLand.Deno (or: irm https://deno.land/install.ps1 | iex)"}}},_9e={upload:["git-annex","gh","aws","deno"],download:["gh"],clone:["git","gh"],push:["git-annex","gh"],publish:["gh","aws"],update:["git","gh"],release:["git","gh"]}});var UW;var BW=O(()=>{UW={name:"nemar-cli",version:"0.10.1
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`))}var qW,_9e,D9e=4000;var af=O(()=>{sr();qW={git:{name:"git",purpose:"version control for dataset metadata",cmd:["git","--version"],required:!0,installInstructions:{macos:"brew install git (or install Xcode Command Line Tools)",linux:"sudo apt-get install git OR sudo dnf install git",windows:"winget install Git.Git (or https://git-scm.com/download/win)"}},"git-annex":{name:"git-annex",purpose:"large-file data transfer (upload/download)",cmd:["git-annex","version"],required:!0,installInstructions:{macos:"brew install git-annex",linux:"sudo apt-get install git-annex OR sudo dnf install git-annex",windows:"Download the installer from https://git-annex.branchable.com/install/Windows/"}},gh:{name:"GitHub CLI (gh)",purpose:"GitHub authentication + repository operations",cmd:["gh","--version"],required:!0,installInstructions:{macos:"brew install gh",linux:"See https://cli.github.com/manual/installation",windows:"winget install GitHub.cli (or: scoop install gh)"}},aws:{name:"AWS CLI",purpose:"S3 data upload/download",cmd:["aws","--version"],required:!0,installInstructions:{macos:"brew install awscli",linux:"pip install awscli OR sudo snap install aws-cli --classic",windows:"winget install Amazon.AWSCLI (or the MSI from https://aws.amazon.com/cli/)"}},deno:{name:"Deno",purpose:"BIDS validation",cmd:["deno","--version"],required:!0,installInstructions:{macos:"brew install deno (or: curl -fsSL https://deno.land/install.sh | sh)",linux:"curl -fsSL https://deno.land/install.sh | sh",windows:"winget install DenoLand.Deno (or: irm https://deno.land/install.ps1 | iex)"}}},_9e={upload:["git-annex","gh","aws","deno"],download:["gh"],clone:["git","gh"],push:["git-annex","gh"],publish:["gh","aws"],update:["git","gh"],release:["git","gh"]}});var UW;var BW=O(()=>{UW={name:"nemar-cli",version:"0.10.1",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","migrations:d1-check":"bun run scripts/d1-migration-check.ts","zarr:geometry-check":"bun run backend/scripts/zarr-geometry-conformance.ts","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit && tsc --noEmit -p backend","generate-openapi":"bun run scripts/generate-openapi.ts",prepublishOnly:"bun run build",prepare:"husky",postinstall:"bun scripts/postinstall-check.mjs",deploy:"wrangler deploy",preview:"wrangler dev"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"CC-BY-NC-ND-4.0",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://docs.nemar.org",engines:{bun:">=1.0.0"},files:["dist","scripts/postinstall-check.mjs","scripts/recover-datasets.json","scripts/withdrawn-datasets.json","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1",inquirer:"^9.2.15",ora:"^8.0.1",semver:"^7.8.5",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@asteasolutions/zod-to-openapi":"^7.3.4","@biomejs/biome":"1.9.4","@types/bun":"latest","@types/inquirer":"^9.0.7","@types/semver":"^7.8.0",ajv:"^8.20.0","ajv-formats":"^3.0.1",bcryptjs:"^3.0.3",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0",yaml:"^2.8.4"}}});var so;var cf=O(()=>{BW();so=UW.version});import{mkdirSync as $9e,readdirSync as C9e,unlinkSync as R9e,writeFileSync as k9e}from"fs";import{join as dD}from"path";function WW(){rl=!0}function aa(){return rl}function KW(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function uf(e){HW=e,vr(`Step: ${e}`)}function YW(){GW=!0}function JW(){return GW}function vr(e){if(rl)process.stderr.write(`[debug] ${e}
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`)}function I9e(e){let t={};for(let[r,n]of Object.entries(e))t[r]=F9e.has(r.toLowerCase())?"[REDACTED]":n;return t}function ZW(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function fD(e,t,r=0){if(r>T9e)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>fD(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[i,o]of Object.entries(t))n[i]=fD(i,o,r+1);return n}if(typeof t==="string"){if(P9e.test(e))return"[REDACTED]";return t.replace(XW,ZW)}return t}function pD(e){return e.replace(N9e,"Bearer [REDACTED]").replace(q9e,"[REDACTED_AWS_KEY]").replace(j9e,"$1[REDACTED]").replace(M9e,"$1$2=[REDACTED]").replace(XW,ZW)}function L9e(e){return pD(e)}function VW(e,t=O9e){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(fD("",n))}catch{}if(r=pD(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function G0(e){if(!rl)return;let t=L9e(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?I9e(e.requestHeaders):void 0,requestBody:VW(e.requestBody),responseBody:VW(e.responseBody)};z0.push(r),vr(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=N(r);z0.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${n}`}),vr(`redaction failed for ${e.method} ${t}: ${n}`)}}async function B9e(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${so}`),e.push(`OS/Arch: ${process.platform}/${process.arch}`),e.push(`Runtime: ${t}`)}catch(t){e.push(`(could not read CLI/OS/runtime info: ${N(t)})`)}e.push(""),e.push("Active account:");try{let t=nt();if(t.apiKey){if(t.username)e.push(` Username: ${t.username}`);if(e.push(` API URL: ${t.apiUrl}`),t.role)e.push(` Role: ${t.role}`);e.push(` Sandbox completed: ${!!t.sandboxCompleted}`)}else e.push(" (not authenticated)")}catch(t){e.push(` (could not read account config: ${N(t)})`)}e.push(""),e.push("External tools:");try{let t=await sf();for(let r of t){let n=r.available?r.version??"installed":r.timedOut?"(timed out)":"not installed";e.push(` ${r.name}: ${n}`)}}catch(t){e.push(` (could not probe external tools: ${N(t)})`)}return e}async function mD(){return(await B9e()).join(`
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`)}async function QW(){if(!rl||V0!==void 0)return;try{V0=await mD()}catch(e){let t=N(e);V0=`(could not build environment report: ${t})`,vr(`environment snapshot failed: ${t}`)}}function eK(e){if(zW.has(e))return{flag:e};for(let t of zW){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function U9e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],i=eK(n);if(!i){t.push(n);continue}if(i.kind==="long-eq")t.push(`${i.flag}=[REDACTED]`);else if(i.kind==="short-attached")t.push(`${i.flag}[REDACTED]`);else if(t.push(n),r+1<e.length)t.push("[REDACTED]"),r++}return t}function V9e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],i=eK(n);if(!i){t.push(n);continue}if(!i.kind&&r+1<e.length)r++}return t}function z9e(e){let t=[];for(let n of V9e(e)){if(n.startsWith("-"))continue;if(t.push(n),t.length===2)break}return(t.length>0?t.join("-"):"nemar").replace(/[^a-zA-Z0-9_-]/g,"_")}function G9e(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${pD(U9e(e).join(" "))}`),r.push(""),r.push(V0??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),z0.length===0)r.push(" (none)");else z0.forEach((n,i)=>{if(r.push(` [${i+1}] ${n.method} ${n.url} -> ${n.status??"ERROR"} (${n.durationMs}ms)`),n.error)r.push(` Error: ${n.error}`);if(n.note)r.push(` Note: ${n.note}`);if(n.requestHeaders)r.push(` Request headers: ${JSON.stringify(n.requestHeaders)}`);if(n.requestBody)r.push(` Request body: ${n.requestBody}`);if(n.responseBody)r.push(` Response body: ${n.responseBody}`)});return r.push(""),r.push(`Failing step: ${HW??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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`}function H9e(e,t){let r;try{r=C9e(e).filter((i)=>i.startsWith("nemar-")&&i.endsWith(".log"))}catch(i){if(i.code!=="ENOENT")vr(`could not list ${e} for log rotation: ${N(i)}`);return}r.sort();let n=r.length-t;for(let i=0;i<n;i++)try{R9e(dD(e,r[i]))}catch(o){if(o.code!=="ENOENT")vr(`could not remove old log ${r[i]}: ${N(o)}`)}}function tK(){return lf}function rK(e,t){if(!rl)return null;let r=dD(hD(),"logs");try{$9e(r,{recursive:!0})}catch(s){return lf=N(s),vr(`could not create log directory ${r}: ${lf}`),null}let i=`nemar-${new Date().toISOString().replace(/[:.]/g,"-")}-${z9e(e)}.log`,o=dD(r,i);try{k9e(o,G9e(e,t),"utf8")}catch(s){return lf=N(s),vr(`could not write log file ${o}: ${lf}`),null}return H9e(r,A9e),o}var A9e=10,O9e=2048,rl=!1,GW=!1,HW,V0,z0,F9e,P9e,XW,T9e=32,N9e,q9e,j9e,M9e,zW,lf;var ao=O(()=>{kt();Si();af();cf();z0=[];F9e=new Set(["authorization","cookie","set-cookie","x-api-key"]);P9e=/^(api[_-]?key|apikey|password|token|secret|access[_-]?key(_id)?|secret[_-]?access[_-]?key|session[_-]?token|authorization|ssh[_-]?key|private[_-]?key|device[_-]?code)$/i,XW=/[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}/g;N9e=/Bearer\s+[A-Za-z0-9\-._~+/=]+/gi,q9e=/\b(?:AKIA|ASIA)[0-9A-Z]{16}\b/g,j9e=/((?:aws_)?secret_access_key["']?\s*[:=]\s*["']?)[A-Za-z0-9/+=]{20,}/gi,M9e=/([?&])(X-Amz-Signature|X-Amz-Security-Token|X-Amz-Credential|Signature|AWSAccessKeyId)=[^&\s"']+/gi;zW=new Set(["-k","--key","--password","--api-key"])});import{chmodSync as W9e,copyFileSync as K9e,existsSync as gD,mkdirSync as Y9e,statSync as J9e}from"fs";import{homedir as H0}from"os";import{join as nl}from"path";function Z9e(e){let t=e.trim().replace(/\/+$/,"");try{let r=new URL(t);return r.protocol=r.protocol.toLowerCase(),r.host=r.host.toLowerCase(),r.toString().replace(/\/+$/,"")}catch{return console.error(`[nemar] could not parse stored apiUrl ${JSON.stringify(e)}; leaving as-is`),t}}function hD(){return process.env.NEMAR_CONFIG_DIR||nl(H0(),".config","nemar")}function e7e(e){if(process.env.NEMAR_CONFIG_DIR)return;let t=nl(e,"config.json");if(gD(t))return;let r=[];if(process.platform==="darwin")r.push(nl(H0(),"Library","Preferences","nemar-nodejs","config.json"));if(process.platform==="win32"){let n=process.env.APPDATA||nl(H0(),"AppData","Roaming");r.push(nl(n,"nemar-nodejs","config.json"))}r.push(nl(H0(),".config","nemar-nodejs","config.json"));for(let n of r)if(gD(n))try{Y9e(e,{recursive:!0}),K9e(n,t),console.error(`[nemar] Config migrated from ${n} to ${t}
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[nemar] You can safely remove the old file.`);return}catch(i){console.error(`[nemar] Failed to migrate config from ${n}:`,i,`
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[nemar] You can manually copy ${n} to ${t}`)}}function bn(){let e=hD();if(df&&nK===e)return df;if(e7e(e),df=new U0({projectName:"nemar",configFileMode:yD,schema:{activeAccount:{type:"string"},accounts:{type:"object"},apiKey:{type:"string"},apiUrl:{type:"string"},username:{type:"string"},email:{type:"string"},githubUsername:{type:"string"},sandboxCompleted:{type:"boolean"},sandboxDatasetId:{type:"string"}},cwd:e}),nK=e,!iK.has(e))iK.add(e),t7e(df.path),n7e(),i7e();return df}function t7e(e){if(process.platform==="win32")return;if(!gD(e))return;try{if((J9e(e).mode&511)!==yD)W9e(e,yD)}catch(t){console.error(`[nemar] could not secure config file permissions for ${e}:`,t)}}function n7e(){let e=bn(),t=e.get("accounts");if(t&&Object.keys(t).length>0)return;let r=e.get("apiKey"),n=e.get("username");if(!r&&!n)return;try{let i=n||"default",o={};for(let s of r7e){let a=e.get(s);if(a!==void 0)o[s]=a}e.store={activeAccount:i,accounts:{[i]:o}}}catch(i){console.error("Config migration failed (legacy config preserved):",i)}}function i7e(){let e=bn(),t=e.store,r=t.accounts,n=!1;if(r)for(let[o,s]of Object.entries(r)){let a=s?.apiUrl;if(!a)continue;if(X9e.has(Z9e(a)))r[o]={...s,apiUrl:il},console.error(`[nemar] migrated stored apiUrl for account "${o}": ${a} -> ${il}`),n=!0}let i=t.apiUrl;if(r&&Object.keys(r).length>0&&i!==void 0){let{apiUrl:o,...s}=t;try{e.store=s,console.error(`[nemar] removed stale top-level apiUrl from config (was: ${i})`),n=!1}catch(a){console.error("API URL cleanup failed (config file unchanged):",a)}}if(n)try{e.store={...e.store,accounts:r}}catch(o){console.error("API URL migration failed (config file unchanged):",o)}}function ff(){return bn().get("activeAccount")}function us(){return bn().get("accounts")||{}}function nt(){let e={apiUrl:il},t=ff();if(!t)return e;return us()[t]||e}function _t(e,t){let r=bn(),n=r.get("activeAccount")||"default",i=r.get("accounts")||{};if(!i[n])i[n]={apiUrl:il};i[n][e]=t,r.store={...r.store,accounts:i,activeAccount:n}}function pf(e){let t=ff();if(!t)return;let r=us();if(r[t])delete r[t][e],bn().set("accounts",r)}function oK(){let e=bn(),t=ff();if(!t){e.clear();return}let r=us();delete r[t];let n=Object.keys(r);if(n.length>0)e.store={...e.store,accounts:r,activeAccount:n[0]};else e.clear()}function sK(){bn().clear()}function Te(){return!!nt().apiKey}function xD(){return bn().path}function mf(){let e=us(),t=ff();return Object.entries(e).map(([r,n])=>({key:r,username:n.username,email:n.email,githubUsername:n.githubUsername,active:r===t,keySource:n.keySource}))}function aK(e){return e.username?.trim()||e.email}function o7e(e){let t=e.trim().toLowerCase();if(!t)return;let r=Object.entries(us()).filter(([,n])=>n.email&&n.email.toLowerCase()===t).map(([n])=>n);if(r.length>1){vr(`findAccountKeyByEmail: ${r.length} accounts share email ${t}: ${r.join(", ")}`);return}return r[0]}function cK(e,t){let r=bn(),n=us(),i;if(n[e])i=e;else if(t.email)i=o7e(t.email);let o=i?n[i]:void 0,s={...o??{apiUrl:il},...t};if(i&&i!==e)delete n[i];return n[e]=s,r.store={...r.store,accounts:n,activeAccount:e},{key:e,previous:o}}function lK(e){let t=e.trim();if(!t)return"unchanged";let r=bn(),n=ff();if(!n||n===t)return"unchanged";let i=us(),o=i[n];if(!o)return"unchanged";if(i[t])return"key_taken";return delete i[n],i[t]={...o,username:t},r.store={...r.store,accounts:i,activeAccount:t},"renamed"}function bD(e){let t=bn(),r=us();if(r[e])return t.store={...t.store,activeAccount:e},r[e];for(let[n,i]of Object.entries(r))if(i.githubUsername===e)return t.store={...t.store,activeAccount:n},i;return null}var il="https://
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[nemar] You can manually copy ${n} to ${t}`)}}function bn(){let e=hD();if(df&&nK===e)return df;if(e7e(e),df=new U0({projectName:"nemar",configFileMode:yD,schema:{activeAccount:{type:"string"},accounts:{type:"object"},apiKey:{type:"string"},apiUrl:{type:"string"},username:{type:"string"},email:{type:"string"},githubUsername:{type:"string"},sandboxCompleted:{type:"boolean"},sandboxDatasetId:{type:"string"}},cwd:e}),nK=e,!iK.has(e))iK.add(e),t7e(df.path),n7e(),i7e();return df}function t7e(e){if(process.platform==="win32")return;if(!gD(e))return;try{if((J9e(e).mode&511)!==yD)W9e(e,yD)}catch(t){console.error(`[nemar] could not secure config file permissions for ${e}:`,t)}}function n7e(){let e=bn(),t=e.get("accounts");if(t&&Object.keys(t).length>0)return;let r=e.get("apiKey"),n=e.get("username");if(!r&&!n)return;try{let i=n||"default",o={};for(let s of r7e){let a=e.get(s);if(a!==void 0)o[s]=a}e.store={activeAccount:i,accounts:{[i]:o}}}catch(i){console.error("Config migration failed (legacy config preserved):",i)}}function i7e(){let e=bn(),t=e.store,r=t.accounts,n=!1;if(r)for(let[o,s]of Object.entries(r)){let a=s?.apiUrl;if(!a)continue;if(X9e.has(Z9e(a)))r[o]={...s,apiUrl:il},console.error(`[nemar] migrated stored apiUrl for account "${o}": ${a} -> ${il}`),n=!0}let i=t.apiUrl;if(r&&Object.keys(r).length>0&&i!==void 0){let{apiUrl:o,...s}=t;try{e.store=s,console.error(`[nemar] removed stale top-level apiUrl from config (was: ${i})`),n=!1}catch(a){console.error("API URL cleanup failed (config file unchanged):",a)}}if(n)try{e.store={...e.store,accounts:r}}catch(o){console.error("API URL migration failed (config file unchanged):",o)}}function ff(){return bn().get("activeAccount")}function us(){return bn().get("accounts")||{}}function nt(){let e={apiUrl:il},t=ff();if(!t)return e;return us()[t]||e}function _t(e,t){let r=bn(),n=r.get("activeAccount")||"default",i=r.get("accounts")||{};if(!i[n])i[n]={apiUrl:il};i[n][e]=t,r.store={...r.store,accounts:i,activeAccount:n}}function pf(e){let t=ff();if(!t)return;let r=us();if(r[t])delete r[t][e],bn().set("accounts",r)}function oK(){let e=bn(),t=ff();if(!t){e.clear();return}let r=us();delete r[t];let n=Object.keys(r);if(n.length>0)e.store={...e.store,accounts:r,activeAccount:n[0]};else e.clear()}function sK(){bn().clear()}function Te(){return!!nt().apiKey}function xD(){return bn().path}function mf(){let e=us(),t=ff();return Object.entries(e).map(([r,n])=>({key:r,username:n.username,email:n.email,githubUsername:n.githubUsername,active:r===t,keySource:n.keySource}))}function aK(e){return e.username?.trim()||e.email}function o7e(e){let t=e.trim().toLowerCase();if(!t)return;let r=Object.entries(us()).filter(([,n])=>n.email&&n.email.toLowerCase()===t).map(([n])=>n);if(r.length>1){vr(`findAccountKeyByEmail: ${r.length} accounts share email ${t}: ${r.join(", ")}`);return}return r[0]}function cK(e,t){let r=bn(),n=us(),i;if(n[e])i=e;else if(t.email)i=o7e(t.email);let o=i?n[i]:void 0,s={...o??{apiUrl:il},...t};if(i&&i!==e)delete n[i];return n[e]=s,r.store={...r.store,accounts:n,activeAccount:e},{key:e,previous:o}}function lK(e){let t=e.trim();if(!t)return"unchanged";let r=bn(),n=ff();if(!n||n===t)return"unchanged";let i=us(),o=i[n];if(!o)return"unchanged";if(i[t])return"key_taken";return delete i[n],i[t]={...o,username:t},r.store={...r.store,accounts:i,activeAccount:t},"renamed"}function bD(e){let t=bn(),r=us();if(r[e])return t.store={...t.store,activeAccount:e},r[e];for(let[n,i]of Object.entries(r))if(i.githubUsername===e)return t.store={...t.store,activeAccount:n},i;return null}var il="https://api.nemar.org",yD=384,X9e,Q9e,put,df=null,nK=null,iK,r7e;var Si=O(()=>{TW();dn();Xu();ao();X9e=new Set(["https://api.osc.earth/nemar","https://nemar-api.neuromechanist.workers.dev","https://nemar-api-dev.shirazi-10f.workers.dev"]);Q9e=M({field:v(),blocks:te(v()).optional(),set_on:te(v()).optional()}).passthrough(),put=M({apiKey:v().optional(),apiUrl:v().url().default(il),username:v().optional(),email:v().email().optional(),githubUsername:v().optional(),sandboxCompleted:De().optional(),sandboxDatasetId:v().optional(),dismissedNoticeIds:te(C()).optional(),serviceAccess:De().optional(),profileGaps:te(Q9e).optional(),orcidVerified:De().optional(),role:v().optional(),accountKind:Ju.optional(),pendingEmailChange:v().email().optional()});iK=new Set;r7e=["apiKey","apiUrl","username","email","githubUsername","sandboxCompleted","sandboxDatasetId","dismissedNoticeIds"]});function W0(e){if(uK)return;uK=!0;let t=l.yellow("\u2500".repeat(60)),r=l.yellow.bold("[MAINTENANCE]"),n=l.dim(`mode: ${e.mode}`),i=e.eta?`
|
|
109
109
|
${l.dim(`eta: ${e.eta}`)}`:"";process.stderr.write(`${t}
|
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110
110
|
${r} ${e.message}
|
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111
|
${n}${i}
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112
112
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${t}
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-
`)}var uK=!1;var _D=O(()=>{Xe()});function dK(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(wD)return vD;return nt().apiUrl||vD}async function I(e,t={},r=!1,n){let i=`${dK()}${e}`,o={"Content-Type":"application/json","X-CLI-Version":so,...t.headers};if(r){let m=nt();if(!m.apiKey&&r===!0)throw new j(401,"Not authenticated. Run 'nemar auth login' first.");if(m.apiKey)o.Authorization=`Bearer ${m.apiKey}`}let s=t.method||"GET",a=typeof t.body==="string"?t.body:void 0,c=Date.now(),u;try{u=await fetch(i,{...t,headers:o})}catch(m){if(aa())G0({method:s,url:i,status:null,durationMs:Date.now()-c,requestHeaders:o,requestBody:a,error:m instanceof Error?m.message:String(m)});throw new j(0,`Network error: Could not connect to ${dK()}`,{originalError:m instanceof Error?m.message:String(m)})}let d;try{d=await u.text()}catch(m){if(aa())G0({method:s,url:i,status:u.status,durationMs:Date.now()-c,requestHeaders:o,requestBody:a,error:m instanceof Error?m.message:String(m)});throw new j(0,"Failed to read response body",{httpStatus:u.status,originalError:m instanceof Error?m.message:String(m)})}if(aa())G0({method:s,url:i,status:u.status,durationMs:Date.now()-c,requestHeaders:o,requestBody:a,responseBody:d});let f;try{f=JSON.parse(d)}catch{throw new j(u.status,`Invalid response from server (status ${u.status})`)}if(!u.ok){if(u.status===503&&(f.mode==="read-only"||f.mode==="full")){let R=typeof f.message==="string"?f.message:"NEMAR is in maintenance mode. Please retry shortly.",E=typeof f.eta==="string"?f.eta:null,F=new ls(f.mode,R,E,f.details);throw W0(F),F}let m=typeof f.block_reason==="string",p=Array.isArray(f.missing)?f.missing.filter((R)=>typeof R==="string"):void 0,g=typeof f.error==="string"&&(dq.includes(f.error)||xq.includes(f.error)),y=typeof f.error==="string"&&(Xm.options.includes(f.error)||Dq.includes(f.error)),x=typeof f.error==="string"&&oq.includes(f.error),w=m||g||y||x||p!==void 0&&typeof f.error==="string"&&uq.includes(f.error)?f.message||f.error:f.error||f.message;if(u.status===404&&f.error==="Not Found"&&typeof f.message==="string")w=`${f.message}. 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I(`/admin/approve/${e}`,{method:"POST"},!0)}async function mK(e){return I(`/admin/approve/by-id/${e}`,{method:"POST"},!0)}async function hK(e){return I(`/admin/revoke/${e}`,{method:"POST"},!0)}async function gK(e){return I(`/admin/revoke/by-id/${e}`,{method:"POST"},!0)}async function yK(e,t){return I(`/admin/users/${e}/role`,{method:"POST",body:JSON.stringify({role:t})},!0)}async function xK(e,t){return I(`/admin/users/${e}/kind`,{method:"POST",body:JSON.stringify({kind:t})},!0)}async function bK(e){return I(`/admin/users/${e}`,{},!0)}async function _K(e,t){return I(`/admin/users/${e}/keys`,{method:"POST",body:JSON.stringify({name:t})},!0,Qm)}async function vK(e){return I(`/admin/users/${e}/keys`,{},!0,Zm)}async function wK(e,t){return I(`/admin/users/${e}/keys/${t}`,{method:"DELETE"},!0)}async function DD(e,t){return I(`/admin/datasets/${e}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:t})},!0)}async function DK(e){return I(`/datasets/${e}/publish`,{method:"POST"},!0)}async function EK(e){return I(`/admin/datasets/${e}/ci`,{},!0)}async function co(e){return I(`/admin/datasets/${e}/ci`,{method:"POST"},!0)}async function ED(e){return I(`/admin/datasets/${e}/ci/validate`,{method:"POST"},!0)}async function SD(e){return I(`/admin/datasets/${e}/ci/sync`,{method:"POST"},!0)}async function SK(e,t){return I(`/admin/datasets/${e}/doi/concept`,{method:"POST",body:JSON.stringify(t)},!0)}async function hf(e){return I(`/admin/datasets/${e}/doi`,{},!0)}async function $D(e,t){return I(`/admin/datasets/${e}/doi/update`,{method:"POST",body:JSON.stringify(t)},!0)}async function $K(e,t){return I(`/admin/datasets/${e}/withdraw`,{method:"POST",body:JSON.stringify({reason:t.reason,dry_run:t.dryRun})},!0)}async function CK(e,t){return I(`/admin/datasets/${e}/restore`,{method:"POST",body:JSON.stringify({dry_run:t.dryRun})},!0)}async function RK(e){return I(`/admin/datasets/${e}/reset`,{method:"POST"},!0)}async function kK(e,t=!1){return I(`/admin/datasets/${e}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:t})},!0)}async function AK(e){return I("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:e})},!0)}async function OK(e){return I("/admin/datasets/import",{method:"POST",body:JSON.stringify(e)},!0)}async function FK(e){return I("/admin/datasets/exemplar",{method:"POST",body:JSON.stringify(e)},!0)}async function IK(e){return I(`/admin/datasets/${e}/exemplar/remint-dois`,{method:"POST"},!0)}async function CD(e,t){let r=new URLSearchParams;if(e)r.set("status",e);if(t!==void 0)r.set("blocklisted",t?"1":"0");let n=r.toString();return I(`/admin/imports${n?`?${n}`:""}`,{},!0)}async function PK(e){return I(`/admin/imports/${e}/rollback`,{method:"POST"},!0)}async function TK(e){return I(`/admin/imports/${e}/retry`,{method:"POST"},!0)}async function RD(e){return 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|
|
113
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+
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new j(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:r,failed:n}}var cl=O(()=>{ds();kt()});async function J0(e){return I(`/datasets/${e}/ci/status`,{},!0)}async function uY(e){return I(`/datasets/${e}/manifest`,{},!0)}async function X0(e,t){return I(`/datasets/${e}/manifest/${t}`,{},!0)}function dY(e){let t=e;if(!t.status)t.status="active";else if(!["active","archived","deleted"].includes(t.status))throw Error(`Invalid dataset status: ${t.status}`);if(!t.visibility)t.visibility="private";else if(!["public","private"].includes(t.visibility))throw Error(`Invalid dataset visibility: ${t.visibility}`);return t}async function ll(e={}){let t=new URLSearchParams;if(e.mine)t.set("mine","true");if(e.search)t.set("search",e.search);if(e.modality)t.set("modality",e.modality);if(e.author)t.set("author",e.author);if(e.task)t.set("task",e.task);if(e.license)t.set("license",e.license);if(e.hasDoi)t.set("has_doi","true");if(e.hasHed)t.set("has_hed","1");if(e.hasZarr)t.set("has_zarr","1");if(e.hasZarrVerified)t.set("has_zarr_verified","1");if(e.dataComplete)t.set("data_complete","1");if(e.recent)t.set("recent",String(e.recent));if(e.sort)t.set("sort",e.sort);if(e.limit!=null)t.set("limit",String(e.limit));if(e.offset!=null)t.set("offset",String(e.offset));if(e.owner)t.set("owner",e.owner);if(e.facets)for(let[i,o]of Object.entries(e.facets))t.set(i,o);if(e.includeUnknown)t.set("include_unknown","1");let r=t.toString()?`?${t.toString()}`:"",n=await I(`/datasets${r}`,{},e.mine?!0:"optional");return n.datasets=n.datasets.map(dY),n}async function fY(e){return I(`/datasets/resolve/${e}`,{},"optional")}async function pY(){return I("/datasets/facets",{signal:AbortSignal.timeout(5000)},"optional",Jm)}async function mY(e,t={}){let r=new URLSearchParams({q:e});if(t.modality)r.set("modality",t.modality);if(t.limit)r.set("limit",String(t.limit));if(t.hasHed)r.set("has_hed","1");if(t.hasZarr)r.set("has_zarr","1");if(t.hasZarrVerified)r.set("has_zarr_verified","1");if(t.author)r.set("author",t.author);if(t.task)r.set("task",t.task);if(t.license)r.set("license",t.license);if(t.hasDoi)r.set("has_doi","true");if(t.dataComplete)r.set("data_complete","1");if(t.recent)r.set("recent",String(t.recent));if(t.facets)for(let[i,o]of Object.entries(t.facets))r.set(i,o);if(t.includeUnknown)r.set("include_unknown","1");return await I(`/datasets/search?${r.toString()}`,{},"optional",gq)}async function At(e){let t=await I(`/datasets/${e}`,{},"optional");return dY(t.dataset)}async function hY(e){return I(`/datasets/${e}/versions`,{},!0)}async function Z0(e){return I("/datasets",{method:"POST",body:JSON.stringify(e)},!0)}async function Q0(e){return I(`/datasets/${e}/finalize`,{method:"POST"},!0)}async function ID(e){return I(`/datasets/${e}/request-access`,{method:"POST"},!0)}async function gY(e,t){let r=t?`?status=${t}`:"";return I(`/datasets/${e}/access-requests${r}`,{},!0)}async function yY(e,t){return I(`/datasets/${e}/access-requests/${t}/approve`,{method:"POST"},!0)}async function xY(e,t){return I(`/datasets/${e}/access-requests/${t}/deny`,{method:"POST"},!0)}async function bY(e,t){return I(`/datasets/${e}/invite`,{method:"POST",body:JSON.stringify({username:t})},!0)}async function _Y(e){return I(`/datasets/${e}/collaborators`,{},!0)}async function vY(e,t){return I(`/admin/datasets/${e}/enrichment`,{method:"POST",body:JSON.stringify(t)},!0)}var Y0;var fs=O(()=>{Ac();ds();Y0=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/});var ul;var $Y=O(()=>{ul=["ci_check","enrichment_check","s3_public_read","repo_public","tag_protect","doi_create","update_metadata","update_readme","create_tag","create_release","upload_to_zenodo","publish_doi","version_doi","s3_lock","sync_nemar","notify_user"]});async function dl(e){return I(`/datasets/${e}/publish/request`,{method:"POST"},!0)}async function RY(e){return I(`/datasets/${e}/publish/status`,{},!0)}async function kY(e){return I(`/datasets/${e}/publish/resend`,{method:"POST"},!0)}async function AY(e){let t=e?`?status=${e}`:"";return I(`/admin/publish/requests${t}`,{},!0)}async function OY(e,t){return I(`/admin/publish/${e}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:t})},!0)}function s7e(e,t=[]){if(e){let r=ul.indexOf(e);if(r>=0)return r+1}return Math.min(t.length+1,ul.length)}function a7e(e){if(!(e instanceof j))return!1;if(e.statusCode===0)return!0;if(e.statusCode===429)return!0;if(e.statusCode>=500&&e.statusCode<600)return!0;if(e.statusCode===403&&/repository has been locked/i.test(e.message))return!0;return!1}async function fl(e,t=!1,r=!1,n=!1,i,o){let c,u,d=0,f=!1,m,p=t,g=[],y;function x(_,w,S,R){if(!o)return;o({step:_,stepIndex:s7e(_,w),stepTotal:ul.length,s3LockLocked:S,s3LockTotal:R,s3LockResumed:_==="s3_lock"&&f?!0:void 0})}for(let _=1;_<=5;_++)try{let w,S=!0;do{if(w=await I(`/admin/publish/${e}/approve`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({resume:S?p:!0,sandbox:r,s3_lock_continuation_token:c,s3_lock_total:u,skip_ci_check:n})},!0),S=!1,w.step_results)g.push(...w.step_results);if(w.s3_lock_total!==void 0)u=w.s3_lock_total;if(w.s3_lock_batch_count!==void 0)d+=w.s3_lock_batch_count;let R=w.step??w.step_results?.[w.step_results.length-1]?.step;if(R&&(R!==m||R==="s3_lock"))x(R,w.steps_completed??[],R==="s3_lock"?d:void 0,R==="s3_lock"?u:void 0),m=R;if(w.hasMore&&w.s3_lock_continuation_token!==void 0)c=w.s3_lock_continuation_token;else break}while(w.hasMore);if(g.length>0)w.step_results=CY(g);return w}catch(w){if(y=w,_===5||!a7e(w)){if(w instanceof j&&g.length>0)w.stepResults=CY(g);throw w}let R=w;if(i?.({attempt:_,maxAttempts:5,delayMs:1e4,step:R.step,error:R.message}),await new Promise((E)=>setTimeout(E,1e4)),p=!0,c!==void 0)f=!0}throw y}function CY(e){let t=new Map;for(let r of e)t.set(r.step,r);return Array.from(t.values())}var gf=O(()=>{$Y();ds();kt()});async function c7e(){try{let{exitCode:e,stderr:t}=await A(["ssh","-T","-o","BatchMode=yes","-o","ConnectTimeout=5","git@github.com"]),r=t.includes("successfully authenticated");if(!r)console.warn("SSH test to github.com failed:",{exitCode:e,stderr:t.trim().slice(0,500)});return{works:r,error:r?void 0:t.trim().slice(0,500)}}catch(e){let t=e instanceof Error?e.message:String(e);return console.warn("SSH test exception:",t),{works:!1,error:t}}}async function yf(){try{let{stdout:e,exitCode:t,stderr:r}=await A(["gh","auth","token"]);if(t!==0)return console.warn("gh CLI returned non-zero exit code:",t),console.warn("stderr:",r),{token:null,error:`gh auth token failed: ${r.trim()||"unknown error"}`};if(!e.trim())return console.warn("gh auth token returned empty output"),{token:null,error:"gh CLI returned empty token"};return{token:e.trim()}}catch(e){let t=e instanceof Error?e.message:String(e);if(console.error("Failed to get GitHub token from gh CLI:",t),t.includes("ENOENT")||t.includes("not found"))return{token:null,error:"gh CLI not installed (command not found)"};return{token:null,error:`gh CLI error: ${t}`}}}async function eg(e){try{let{stdout:t,exitCode:r,stderr:n}=await A(["gh","api","user","--jq",".login"]);if(r!==0){if(n.includes("not logged in")||n.includes("auth login"))return{authenticated:!1,error:"gh CLI not authenticated. Run 'gh auth login' to authenticate."};return{authenticated:!1,error:`gh CLI error: ${n.trim()||"unknown error"}`}}let i=t.trim();if(!i)return{authenticated:!1,error:"gh CLI returned empty username"};if(e){let o=i.toLowerCase()===e.toLowerCase();return{authenticated:!0,username:i,matches:o,error:o?void 0:`gh CLI authenticated as '${i}', expected '${e}'`}}return{authenticated:!0,username:i}}catch(t){let r=t instanceof Error?t.message:String(t);if(r.includes("ENOENT")||r.includes("not found"))return{authenticated:!1,error:"gh CLI not installed. Install from https://cli.github.com/"};return{authenticated:!1,error:`Failed to verify gh CLI: ${r}`}}}async function tg(e){if(!/^[a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+$/.test(e))return{accepted:!1,error:`Invalid repository format: ${e}`};let{stdout:t,exitCode:r,stderr:n}=await A(["gh","api","/user/repository_invitations"]);if(r!==0){if(n.includes("not logged in")||n.includes("auth login"))return{accepted:!1,error:"gh CLI not authenticated. Run 'gh auth login' to authenticate."};if(n.includes("API rate limit")||n.includes("403"))return{accepted:!1,error:"GitHub API rate limit exceeded. Please try again in a few minutes."};if(n.includes("ENOENT")||n.includes("not found"))return{accepted:!1,error:"gh CLI not installed. Install from https://cli.github.com/"};return{accepted:!1,error:`Failed to list invitations: ${n.trim()||"unknown error"}`}}let i=null;try{i=JSON.parse(t||"[]").find((u)=>u.repository.full_name===e)?.id??null}catch(a){let c=a instanceof Error?a.message:String(a);return console.error("Failed to parse GitHub invitations response:",c),console.error(" Raw response (first 500 chars):",(t||"").slice(0,500)),{accepted:!1,error:`Failed to parse GitHub API response: ${c}`}}if(!i){let{exitCode:a}=await A(["gh","api",`/repos/${e}`,"--silent"]);if(a===0)return{accepted:!0,alreadyCollaborator:!0};return{accepted:!1,error:`No pending invitation found for ${e}. You may need to accept it manually via GitHub.`}}let{exitCode:o,stderr:s}=await A(["gh","api","--method","PATCH",`/user/repository_invitations/${i}`]);if(o!==0)return{accepted:!1,error:`Failed to accept invitation: ${s.trim()||"unknown error"}`};return{accepted:!0}}async function Ci(e,t,r="origin"){let n=t;if(process.env.GH_TOKEN&&t.startsWith("git@github.com:")){let i=process.env.GH_TOKEN.trim();if(!i||/\s/.test(i))return{success:!1,error:"GH_TOKEN environment variable is set but appears malformed (empty or contains whitespace)"};n=`https://github.com/${t.replace("git@github.com:","")}`,await A(["git","config","credential.https://github.com.helper",`!printf 'username=x-access-token\\npassword=${i}'`],{cwd:e})}else if(t.startsWith("git@github.com:")){let i=t.replace("git@github.com:",""),o=await yf();if(o.token)n=`https://github.com/${i}`,await A(["git","config","credential.https://github.com.helper",`!printf 'username=x-access-token\\npassword=${o.token}'`],{cwd:e});else{let s=await c7e();if(s.works)n=t;else return{success:!1,error:`GitHub authentication not configured.
|
|
114
114
|
|
|
115
115
|
gh CLI failed: ${o.error||"could not get token"}
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|
116
116
|
SSH failed: ${s.error||"could not connect"}
|