Merge branch 'test_compare_annotation_children' into gff-conversion-test

GMOD · Sep 3, 2024 · a438acf · a438acf
2 parents bb62e79 + 08590d4
commit a438acf
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diff --git a/.github/workflows/deploy/Dockerfile b/.github/workflows/deploy/Dockerfile
@@ -3,6 +3,7 @@ ARG JBROWSE_VERSION
 COPY ./httpd.conf /usr/local/apache2/conf/httpd.conf
 COPY ./jbrowse-plugin-apollo.umd.development.js /usr/local/apache2/htdocs/
 COPY ./jbrowse-plugin-apollo.umd.production.min.js /usr/local/apache2/htdocs/
+COPY ./jbrowse-plugin-apollo.umd.production.min.js /usr/local/apache2/htdocs/apollo.js
 WORKDIR /usr/local/apache2/htdocs/
 RUN <<EOF
 set -o errexit

diff --git a/.github/workflows/deploy/compose.yml b/.github/workflows/deploy/compose.yml
@@ -12,6 +12,7 @@ services:
       FILE_UPLOAD_FOLDER: /data/uploads
       LOG_LEVELS: error,warn,log,debug
       ALLOW_GUEST_USER: true
+      DEFAULT_NEW_USER_ROLE: user
       URL: ${URL}
       JWT_SECRET: ${JWT_SECRET}
       SESSION_SECRET: ${SESSION_SECRET}

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -6,18 +6,26 @@ on:
 
 jobs:
   publish-npm:
-    name: Publish to npm
+    name: Publish to NPM
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - name: Check out
+        uses: actions/checkout@v4
       # Setup .npmrc file to publish to npm
-      - uses: actions/setup-node@v4
+      - name: Use Node.js 18.x
+        uses: actions/setup-node@v4
         with:
           node-version: 18
           registry-url: https://registry.npmjs.org
           scope: '@apollo-annotation'
-      - run: yarn --immutable
-      - run: |
+          cache: yarn
+      - name: Install
+        run: yarn --immutable
+      - name: Build shared
+        run: yarn build
+        working-directory: packages/apollo-shared
+      - name: Publish
+        run: |
           yarn config set npmAuthToken ${{ secrets.NPM_TOKEN }}
           yarn workspaces foreach --no-private --all npm publish --tolerate-republish
         env:

diff --git a/.prettierrc.js b/.prettierrc.js
diff --git a/.prettierrc.mjs b/.prettierrc.mjs
@@ -0,0 +1,19 @@
+import packagejson from 'prettier-plugin-packagejson'
+/**
+ * @see https://prettier.io/docs/en/configuration.html
+ * @type {import("prettier").Config}
+ */
+const config = {
+  semi: false,
+  singleQuote: true,
+  proseWrap: 'always',
+  overrides: [
+    {
+      files: ['.devcontainer/**/*.json', '.vscode/*.json', '**/tsconfig*.json'],
+      options: { parser: 'jsonc' },
+    },
+  ],
+  plugins: [packagejson],
+}
+
+export default config
diff --git a/.yarn/sdks/eslint/bin/eslint.js b/.yarn/sdks/eslint/bin/eslint.js
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
 // Defer to the real eslint/bin/eslint.js your application uses
-module.exports = absRequire(`eslint/bin/eslint.js`);
+module.exports = wrapWithUserWrapper(absRequire(`eslint/bin/eslint.js`));
diff --git a/.yarn/sdks/eslint/lib/api.js b/.yarn/sdks/eslint/lib/api.js
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
 // Defer to the real eslint your application uses
-module.exports = absRequire(`eslint`);
+module.exports = wrapWithUserWrapper(absRequire(`eslint`));
diff --git a/.yarn/sdks/eslint/lib/unsupported-api.js b/.yarn/sdks/eslint/lib/unsupported-api.js
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
 // Defer to the real eslint/use-at-your-own-risk your application uses
-module.exports = absRequire(`eslint/use-at-your-own-risk`);
+module.exports = wrapWithUserWrapper(absRequire(`eslint/use-at-your-own-risk`));
diff --git a/.yarn/sdks/eslint/package.json b/.yarn/sdks/eslint/package.json
@@ -1,6 +1,6 @@
 {
   "name": "eslint",
-  "version": "8.51.0-sdk",
+  "version": "8.57.0-sdk",
   "main": "./lib/api.js",
   "type": "commonjs",
   "bin": {

diff --git a/.yarn/sdks/prettier/bin/prettier.cjs b/.yarn/sdks/prettier/bin/prettier.cjs
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
 // Defer to the real prettier/bin/prettier.cjs your application uses
-module.exports = absRequire(`prettier/bin/prettier.cjs`);
+module.exports = wrapWithUserWrapper(absRequire(`prettier/bin/prettier.cjs`));
diff --git a/.yarn/sdks/prettier/index.cjs b/.yarn/sdks/prettier/index.cjs
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
 // Defer to the real prettier your application uses
-module.exports = absRequire(`prettier`);
+module.exports = wrapWithUserWrapper(absRequire(`prettier`));
diff --git a/.yarn/sdks/prettier/package.json b/.yarn/sdks/prettier/package.json
@@ -1,6 +1,6 @@
 {
   "name": "prettier",
-  "version": "3.2.5-sdk",
+  "version": "3.3.2-sdk",
   "main": "./index.cjs",
   "type": "commonjs",
   "bin": "./bin/prettier.cjs"

diff --git a/.yarn/sdks/typescript/bin/tsc b/.yarn/sdks/typescript/bin/tsc
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
 // Defer to the real typescript/bin/tsc your application uses
-module.exports = absRequire(`typescript/bin/tsc`);
+module.exports = wrapWithUserWrapper(absRequire(`typescript/bin/tsc`));
diff --git a/.yarn/sdks/typescript/bin/tsserver b/.yarn/sdks/typescript/bin/tsserver
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
 // Defer to the real typescript/bin/tsserver your application uses
-module.exports = absRequire(`typescript/bin/tsserver`);
+module.exports = wrapWithUserWrapper(absRequire(`typescript/bin/tsserver`));
diff --git a/.yarn/sdks/typescript/lib/tsc.js b/.yarn/sdks/typescript/lib/tsc.js
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
 // Defer to the real typescript/lib/tsc.js your application uses
-module.exports = absRequire(`typescript/lib/tsc.js`);
+module.exports = wrapWithUserWrapper(absRequire(`typescript/lib/tsc.js`));
diff --git a/.yarn/sdks/typescript/lib/tsserver.js b/.yarn/sdks/typescript/lib/tsserver.js
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,7 +24,15 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
-const moduleWrapper = tsserver => {
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
+const moduleWrapper = exports => {
+  return wrapWithUserWrapper(moduleWrapperFn(exports));
+};
+
+const moduleWrapperFn = tsserver => {
   if (!process.versions.pnp) {
     return tsserver;
   }

diff --git a/.yarn/sdks/typescript/lib/tsserverlibrary.js b/.yarn/sdks/typescript/lib/tsserverlibrary.js
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,7 +24,15 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
-const moduleWrapper = tsserver => {
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
+const moduleWrapper = exports => {
+  return wrapWithUserWrapper(moduleWrapperFn(exports));
+};
+
+const moduleWrapperFn = tsserver => {
   if (!process.versions.pnp) {
     return tsserver;
   }

diff --git a/.yarn/sdks/typescript/lib/typescript.js b/.yarn/sdks/typescript/lib/typescript.js
@@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`);
 const relPnpApiPath = "../../../../.pnp.cjs";
 
 const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`);
 const absRequire = createRequire(absPnpApiPath);
 
 const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`);
@@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) {
   }
 }
 
+const wrapWithUserWrapper = existsSync(absUserWrapperPath)
+  ? exports => absRequire(absUserWrapperPath)(exports)
+  : exports => exports;
+
 // Defer to the real typescript your application uses
-module.exports = absRequire(`typescript`);
+module.exports = wrapWithUserWrapper(absRequire(`typescript`));
diff --git a/.yarn/sdks/typescript/package.json b/.yarn/sdks/typescript/package.json
@@ -1,6 +1,6 @@
 {
   "name": "typescript",
-  "version": "5.2.2-sdk",
+  "version": "5.5.3-sdk",
   "main": "./lib/typescript.js",
   "type": "commonjs",
   "bin": {

diff --git a/package.json b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "apollo3",
+  "private": true,
   "description": "Monorepo containing Apollo front and back end code",
-  "packageManager": "[email protected]",
   "workspaces": [
     "packages/*"
   ],
@@ -42,10 +42,11 @@
     "lint-staged": "^15.2.2",
     "npm-run-all": "^4.1.5",
     "prettier": "^3.3.2",
+    "prettier-plugin-packagejson": "^2.5.2",
     "react": "^18.2.0",
     "tsx": "^4.6.2",
     "typescript": "^5.5.3",
     "yargs": "^17.7.2"
   },
-  "private": true
+  "packageManager": "[email protected]"
 }
diff --git a/packages/apollo-cli/README.md b/packages/apollo-cli/README.md
@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.1.18 linux-x64 node-v20.14.0
+@apollo-annotation/cli/0.1.19 linux-x64 node-v20.13.0
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND