@apollo-annotation/cli 0.3.5 → 0.3.6

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.5 linux-x64 node-v18.20.8
+@apollo-annotation/cli/0.3.6 linux-x64 node-v18.20.8
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -114,7 +114,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -150,7 +150,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -192,7 +192,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -220,7 +220,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -242,7 +242,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -277,7 +277,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -301,7 +301,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -353,7 +353,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo export gff3 ASSEMBLY`
 
@@ -381,7 +381,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/export/gff3.ts)_
+[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/export/gff3.ts)_
 
 ## `apollo feature add-child`
 
@@ -412,7 +412,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -445,7 +445,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -476,7 +476,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -500,7 +500,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -542,7 +542,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -582,7 +582,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -616,7 +616,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -640,7 +640,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -674,7 +674,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -702,7 +702,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -733,7 +733,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -784,7 +784,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -811,7 +811,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -839,7 +839,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -866,7 +866,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -903,7 +903,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -950,7 +950,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -979,7 +979,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -1018,7 +1018,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1048,7 +1048,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1079,7 +1079,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1111,7 +1111,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1133,7 +1133,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1169,6 +1169,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.5/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

package/dist/baseCommand.d.ts

@@ -1,4 +1,4 @@
-import { Command, Interfaces } from '@oclif/core';
+import { Command, type Interfaces } from '@oclif/core';
 export type Flags<T extends typeof Command> = Interfaces.InferredFlags<(typeof BaseCommand)['baseFlags'] & T['flags']>;
 export type Args<T extends typeof Command> = Interfaces.InferredArgs<T['args']>;
 export declare abstract class BaseCommand<T extends typeof Command> extends Command {

package/dist/commands/export/gff3.js

@@ -1,8 +1,8 @@
+import { Readable } from 'node:stream';
 import { Args, Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
 import { convertAssemblyNameToId, createFetchErrorMessage, idReader, localhostToAddress, } from '../../utils.js';
-import { Readable } from 'node:stream';
 export default class Get extends BaseCommand {
     static description = 'Export the annotations for an assembly to stdout as gff3';
     static examples = [

package/dist/commands/feature/add-child.js

@@ -1,5 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { fetch } from 'undici';

package/dist/commands/feature/search.js

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';

package/dist/commands/jbrowse/set-config.js

@@ -3,7 +3,7 @@ import { Args } from '@oclif/core';
 import { Agent, fetch } from 'undici';
 import { ConfigError } from '../../ApolloConf.js';
 import { BaseCommand } from '../../baseCommand.js';
-import { localhostToAddress, createFetchErrorMessage } from '../../utils.js';
+import { createFetchErrorMessage, localhostToAddress } from '../../utils.js';
 export default class SetConfig extends BaseCommand {
     static summary = 'Set JBrowse configuration';
     static description = 'Set JBrowse configuration in Apollo collaboration server';

package/dist/commands/refseq/add-alias.js

@@ -1,9 +1,9 @@
 import * as fs from 'node:fs';
-import { Agent, fetch } from 'undici';
 import { Args, Flags } from '@oclif/core';
+import { Agent, fetch } from 'undici';
+import { ConfigError } from '../../ApolloConf.js';
 import { BaseCommand } from '../../baseCommand.js';
 import { createFetchErrorMessage, localhostToAddress, queryApollo, } from '../../utils.js';
-import { ConfigError } from '../../ApolloConf.js';
 export default class AddRefNameAlias extends BaseCommand {
     static summary = 'Add reference name aliases from a file';
     static description = 'Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the same thing render properly. This command reads a file with reference name aliases and adds them to the database.';

package/dist/test/test.js

@@ -16,11 +16,10 @@
  * yarn test:cli --test-name-pattern='Print help|Feature get'
  */
 import assert from 'node:assert';
-import { before, beforeEach, afterEach, describe } from 'node:test';
-import { Shell } from './utils.js';
-import fs from 'node:fs';
 import * as crypto from 'node:crypto';
-import path from 'node:path';
+import fs from 'node:fs';
+import { afterEach, before, beforeEach, describe } from 'node:test';
+import { Shell } from './utils.js';
 const apollo = 'yarn dev';
 const P = '--profile testAdmin';
 let configFile = '';
@@ -28,7 +27,7 @@ let configFileBak = '';
 void describe('Test CLI', () => {
     before(() => {
         configFile = new Shell(`${apollo} config --get-config-file`).stdout.trim();
-        configFileBak = `${path.basename(configFile)}.bak`;
+        configFileBak = `${configFile}.bak`;
         if (fs.existsSync(configFileBak)) {
             throw new Error(`Backup config file ${configFileBak} already exists. If safe to do so, delete it before testing`);
         }
@@ -308,12 +307,12 @@ void describe('Test CLI', () => {
         assert.ok(p.returncode != 0);
     });
     void globalThis.itName('Detect missing external index', () => {
-        const p = new Shell(`${apollo} assembly add-from-fasta ${P} -a vv1 -f https://raw.githubusercontent.com/GMOD/Apollo3/refs/heads/main/packages/apollo-cli/test_data/tiny.fasta`, false);
+        const p = new Shell(`${apollo} assembly add-from-fasta ${P} -a vv1 -f http://localhost:3131/tiny.fasta`, false);
         assert.ok(p.returncode != 0);
         assert.ok(p.stderr.includes('Index file') && p.stderr.includes('does not exist'));
     });
     void globalThis.itName('Editable sequence not allowed with external source', () => {
-        const cmd = `${apollo} assembly add-from-fasta ${P} -a vv1 -f https://raw.githubusercontent.com/GMOD/Apollo3/refs/heads/main/packages/apollo-cli/test_data/tiny.fasta.gz`;
+        const cmd = `${apollo} assembly add-from-fasta ${P} -a vv1 -f http://localhost:3131/tiny.fasta.gz`;
         new Shell(cmd);
         const p = new Shell(`${cmd} -e`, false);
         assert.ok(p.returncode != 0);
@@ -983,7 +982,7 @@ void describe('Test CLI', () => {
         assert.ok(!gff.includes('##FASTA\n'));
     });
     void globalThis.itName('Export gff3 from external assembly', () => {
-        new Shell(`${apollo} assembly add-from-fasta ${P} https://raw.githubusercontent.com/GMOD/Apollo3/refs/heads/main/packages/apollo-cli/test_data/tiny.fasta.gz -a vv1 -f`);
+        new Shell(`${apollo} assembly add-from-fasta ${P} http://localhost:3131/tiny.fasta.gz -a vv1 -f`);
         new Shell(`${apollo} feature import ${P} test_data/tiny.fasta.gff3 -a vv1`);
         let p = new Shell(`${apollo} export gff3 ${P} vv1 --include-fasta`);
         let gff = p.stdout;

package/dist/test/test_docker.js

@@ -1,8 +1,8 @@
 import assert from 'node:assert';
-import { after, before, describe } from 'node:test';
-import { Shell } from './utils.js';
 import fs from 'node:fs';
 import path from 'node:path';
+import { after, before, describe } from 'node:test';
+import { Shell } from './utils.js';
 const hostTmpDir = path.resolve('tmpTestDocker');
 const hostDataDir = path.resolve('test_data');
 const apollo = `docker run --network host -v ${hostTmpDir}:/root/.config/apollo-cli -v ${hostDataDir}:/data apollo`;

package/dist/utils.d.ts

@@ -1,8 +1,8 @@
-import EventEmitter from 'node:events';
-import type { SerializedAddAssemblyAndFeaturesFromFileChange, SerializedAddAssemblyFromExternalChange, SerializedAddAssemblyFromFileChange } from '@apollo-annotation/shared';
-import { Response } from 'undici';
+import type EventEmitter from 'node:events';
+import { type ApolloAssemblySnapshot } from '@apollo-annotation/mst';
+import { type SerializedAddAssemblyAndFeaturesFromFileChange, type SerializedAddAssemblyFromExternalChange, type SerializedAddAssemblyFromFileChange } from '@apollo-annotation/shared';
+import { type Response } from 'undici';
 import { ApolloConf } from './ApolloConf.js';
-import { ApolloAssemblySnapshot } from '@apollo-annotation/mst';
 export declare const CLI_SERVER_ADDRESS = "http://127.0.0.1:5657";
 export declare const CLI_SERVER_ADDRESS_CALLBACK = "http://127.0.0.1:5657/auth/callback";
 export declare class CheckError extends Error {

package/dist/utils.js

@@ -1,6 +1,6 @@
 import * as crypto from 'node:crypto';
 import * as fs from 'node:fs';
-import { stdin, stderr } from 'node:process';
+import { stderr, stdin } from 'node:process';
 import { Agent, fetch } from 'undici';
 import { ApolloConf, ConfigError } from './ApolloConf.js';
 export const CLI_SERVER_ADDRESS = 'http://127.0.0.1:5657';

package/oclif.manifest.json

@@ -738,6 +738,51 @@
         "gff3.js"
       ]
     },
+    "change:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such cases you need to use the assembly ID.",
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Get changes only for these assembly names or IDs (but see description)",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "change:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get list of changes",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "change",
+        "get.js"
+      ]
+    },
     "feature:add-child": {
       "aliases": [],
       "args": {},
@@ -1540,51 +1585,6 @@
         "search.js"
       ]
     },
-    "change:get": {
-      "aliases": [],
-      "args": {},
-      "description": "Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such cases you need to use the assembly ID.",
-      "flags": {
-        "profile": {
-          "description": "Use credentials from this profile",
-          "name": "profile",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "config-file": {
-          "description": "Use this config file (mostly for testing)",
-          "name": "config-file",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "assembly": {
-          "char": "a",
-          "description": "Get changes only for these assembly names or IDs (but see description)",
-          "name": "assembly",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "change:get",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Get list of changes",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "change",
-        "get.js"
-      ]
-    },
     "file:delete": {
       "aliases": [],
       "args": {},
@@ -2106,5 +2106,5 @@
       ]
     }
   },
-  "version": "0.3.5"
+  "version": "0.3.6"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.3.5",
+  "version": "0.3.6",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",
@@ -88,8 +88,8 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.5",
-    "@apollo-annotation/shared": "^0.3.5",
+    "@apollo-annotation/mst": "^0.3.6",
+    "@apollo-annotation/shared": "^0.3.6",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
@@ -107,6 +107,7 @@
     "prettier": "^3.3.2",
     "react-dom": "^18.2.0",
     "rxjs": "^7.4.0",
+    "serve": "^14.0.1",
     "shx": "^0.3.3",
     "ts-node": "^10.3.0",
     "tsx": "^4.6.2",