@cyanheads/ensembl-mcp-server 0.1.1 → 0.1.3
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/AGENTS.md +1 -1
- package/CLAUDE.md +1 -1
- package/README.md +24 -1
- package/changelog/0.1.x/0.1.2.md +17 -0
- package/changelog/0.1.x/0.1.3.md +12 -0
- package/dist/mcp-server/tools/definitions/query-region.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/query-region.tool.js +4 -2
- package/dist/mcp-server/tools/definitions/query-region.tool.js.map +1 -1
- package/package.json +2 -2
- package/server.json +9 -3
package/AGENTS.md
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# Developer Protocol
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**Server:** ensembl-mcp-server
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**Version:** 0.1.
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**Version:** 0.1.3
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
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package/CLAUDE.md
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# Developer Protocol
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**Server:** ensembl-mcp-server
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**Version:** 0.1.
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**Version:** 0.1.3
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
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package/README.md
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<div align="center">
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/ensembl-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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</div>
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<div align="center">
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**Public Hosted Server:** [https://ensembl.caseyjhand.com/mcp](https://ensembl.caseyjhand.com/mcp)
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</div>
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---
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## Tools
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## Getting started
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### Public Hosted Instance
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A public instance is available at `https://ensembl.caseyjhand.com/mcp` — no installation required. Point any MCP client at it via Streamable HTTP:
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```json
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{
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"mcpServers": {
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"ensembl-mcp-server": {
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"type": "streamable-http",
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"url": "https://ensembl.caseyjhand.com/mcp"
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}
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}
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}
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```
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### Self-Hosted / Local
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Add the following to your MCP client configuration file.
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```json
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---
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summary: "Public hosted endpoint at ensembl.caseyjhand.com/mcp"
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breaking: false
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security: false
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---
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# 0.1.2 — 2026-06-06
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## Added
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- **Public hosted endpoint** — `server.json` `remotes` array with `https://ensembl.caseyjhand.com/mcp` (streamable-http).
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- **README hosted instance** — centered link block after badges; "Public Hosted Instance" subsection under Getting Started with streamable-http client config.
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## Changed
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- `@types/node` ^25.9.1 → ^25.9.2 (dev dep).
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- `@cyanheads/mcp-ts-core` held at `^0.9.21`; added to `devcheck.config.json` outdated allowlist.
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---
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summary: "ensembl_query_region: invalid region strings raise the invalid_region contract; empty-result notice includes chr-prefix guidance"
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breaking: false
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security: false
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---
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# 0.1.3 — 2026-06-06
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## Fixed
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- **`ensembl_query_region`** — Ensembl's `"No slice found for location"` error now maps to `ctx.fail('invalid_region', …)` (code -32007) instead of falling through as a generic NotFound with `data.reason: null`. Resolves [#1](https://github.com/cyanheads/ensembl-mcp-server/issues/1).
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- **`ensembl_query_region` empty-result notice** — expanded from a vague intergenic note to include the chr-prefix convention (`13`, not `chr13`) and a pointer to `ensembl_lookup_gene` for coordinate lookup. Notice text now surfaces in both `structuredContent.notice` and `content[]`. Resolves [#2](https://github.com/cyanheads/ensembl-mcp-server/issues/2).
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{"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8BjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8BjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+J7B,CAAC"}
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.catch((err) => {
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const msg = err instanceof Error ? err.message : String(err);
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if (/invalid.*region|coordinate|parse/i.test(msg) ||
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/is not a valid start|is not a valid end|is not a valid chr/i.test(msg)
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/is not a valid start|is not a valid end|is not a valid chr/i.test(msg) ||
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/no slice found/i.test(msg)) {
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throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}`);
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}
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if (/species|invalid|unrecognized/i.test(msg)) {
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});
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if (features.length === 0) {
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ctx.enrich.notice(`No ${input.feature.join(', ')} features found in ${input.region} for ${input.species}. ` +
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'The region may be intergenic
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'The region may be intergenic. Chromosome names use no "chr" prefix for vertebrates ' +
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'(e.g. 13, not chr13). Use ensembl_lookup_gene to confirm locus coordinates.');
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}
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else if (features.length > 1000) {
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ctx.enrich.notice(`Large result set (${features.length} features). ` +
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{"version":3,"file":"query-region.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,aAAa,GAAG,CAAC,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,YAAY,EAAE,MAAM,CAAU,CAAC;AAEzF,MAAM,aAAa,GAAG,CAAC,CAAC,MAAM,CAAC;IAC7B,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uDAAuD,CAAC;IAC3F,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;IACjF,WAAW,EAAE,CAAC;SACX,MAAM,EAAE;SACR,QAAQ,CAAC,iEAAiE,CAAC;IAC9E,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,4DAA4D,CAAC;IACzE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACtE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;IACzE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;IACrE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;IACjF,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,sDAAsD,CAAC;IACnE,oBAAoB,EAAE,CAAC;SACpB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC,CAAC;SAC5E,QAAQ,EAAE;SACV,QAAQ,CAAC,+EAA+E,CAAC;CAC7F,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,sBAAsB;IAC7B,WAAW,EACT,mGAAmG;QACnG,kGAAkG;QAClG,wGAAwG;QACxG,kGAAkG;QAClG,oGAAoG;QACpG,qGAAqG;QACrG,sEAAsE;IACxE,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,CACP,wEAAwE;YACtE,oDAAoD,CACvD;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,CACP,sEAAsE;YACpE,yFAAyF;YACzF,wFAAwF,CAC3F;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,IAAI,CAAC,aAAa,CAAC;aACnB,QAAQ,CACP,+EAA+E,CAChF,CACJ;aACA,OAAO,CAAC,CAAC,MAAM,CAAC,CAAC;aACjB,QAAQ,CACP,mDAAmD;YACjD,mFAAmF;YACnF,kFAAkF,CACrF;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8DAA8D;YAC5D,kFAAkF,CACrF;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,aAAa,CAAC,QAAQ,CAAC,0DAA0D,CAAC,CAAC;aACzF,QAAQ,CAAC,iDAAiD,CAAC;QAC9D,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CACP,qFAAqF,CACtF;QACH,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAC/D,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACrD,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;KACpF;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,gBAAgB;YACxB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,wEAAwE;YAC9E,QAAQ,EACN,4DAA4D;gBAC5D,4EAA4E;gBAC5E,8EAA8E;SACjF;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EACN,2FAA2F;SAC9F;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,iBAAiB,EAAE;YAC9B,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,QAAQ,EAAE,KAAK,CAAC,OAAO;YACvB,OAAO,EAAE,KAAK,CAAC,OAAO;SACvB,CAAC,CAAC;QACH,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,QAAQ,GAAG,MAAM,OAAO;aAC3B,WAAW,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC;aAC3E,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IACE,mCAAmC,CAAC,IAAI,CAAC,GAAG,CAAC;gBAC7C,6DAA6D,CAAC,IAAI,CAAC,GAAG,CAAC,
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/ensembl-mcp-server",
|
|
3
|
-
"version": "0.1.
|
|
3
|
+
"version": "0.1.3",
|
|
4
4
|
"mcpName": "io.github.cyanheads/ensembl-mcp-server",
|
|
5
5
|
"description": "Look up genes, fetch sequences, predict variant consequences, find orthologs and cross-database xrefs via Ensembl REST via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
|
@@ -96,7 +96,7 @@
|
|
|
96
96
|
},
|
|
97
97
|
"devDependencies": {
|
|
98
98
|
"@biomejs/biome": "^2.4.16",
|
|
99
|
-
"@types/node": "^25.9.
|
|
99
|
+
"@types/node": "^25.9.2",
|
|
100
100
|
"depcheck": "^1.4.7",
|
|
101
101
|
"ignore": "^7.0.5",
|
|
102
102
|
"tsc-alias": "^1.8.17",
|
package/server.json
CHANGED
|
@@ -6,14 +6,20 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/ensembl-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "0.1.
|
|
9
|
+
"version": "0.1.3",
|
|
10
|
+
"remotes": [
|
|
11
|
+
{
|
|
12
|
+
"type": "streamable-http",
|
|
13
|
+
"url": "https://ensembl.caseyjhand.com/mcp"
|
|
14
|
+
}
|
|
15
|
+
],
|
|
10
16
|
"packages": [
|
|
11
17
|
{
|
|
12
18
|
"registryType": "npm",
|
|
13
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
14
20
|
"identifier": "@cyanheads/ensembl-mcp-server",
|
|
15
21
|
"runtimeHint": "bun",
|
|
16
|
-
"version": "0.1.
|
|
22
|
+
"version": "0.1.3",
|
|
17
23
|
"packageArguments": [
|
|
18
24
|
{
|
|
19
25
|
"type": "positional",
|
|
@@ -49,7 +55,7 @@
|
|
|
49
55
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
50
56
|
"identifier": "@cyanheads/ensembl-mcp-server",
|
|
51
57
|
"runtimeHint": "bun",
|
|
52
|
-
"version": "0.1.
|
|
58
|
+
"version": "0.1.3",
|
|
53
59
|
"packageArguments": [
|
|
54
60
|
{
|
|
55
61
|
"type": "positional",
|