Add missing files to update

README.txt

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+Themes allow you to change the look and feel of your Drupal site. You can use
+themes contributed by others or create your own.
+
+WHAT TO PLACE IN THIS DIRECTORY?
+--------------------------------
+
+Placing downloaded and custom themes in this directory separates downloaded and
+custom themes from Drupal core's themes. This allows Drupal core to be updated
+without overwriting these files.
+
+DOWNLOAD ADDITIONAL THEMES
+--------------------------
+
+Contributed themes from the Drupal community may be downloaded at
+https://www.drupal.org/project/project_theme.
+
+MULTISITE CONFIGURATION
+-----------------------
+
+In multisite configurations, themes found in this directory are available to
+all sites. You may also put themes in the sites/all/themes directory, and the
+versions in sites/all/themes will take precedence over versions of the same
+themes that are here. Alternatively, the sites/your_site_name/themes directory
+pattern may be used to restrict themes to a specific site instance.
+
+MORE INFORMATION
+-----------------
+
+Refer to the "Appearance" section of the README.md in the Drupal root directory
+for further information on customizing the appearance of Drupal with custom
+themes.

biodatapt-theme/README.md

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+# BioData.pt Theme for Drupal
+
+[![Deploy](https://github.com/BioData-PT/biodatapt-theme/actions/workflows/ssh-deploy.yml/badge.svg)](https://github.com/BioData-PT/biodatapt-theme/actions/workflows/ssh-deploy.yml)
+
+Maintainer: [Gil Poiares-Oliveira](mailto:[email protected]) (INESC-ID | BioData.pt | ELIXIR Portugal)
+
+All BioData.pt logos and imagery are © Associação BIP4DAB - all rights reserved.
+
+Code is available under a [GPL 2.0 license](LICENSE.txt).
+
+Based on [Vartheme BS5](https://www.drupal.org/project/vartheme_bs5). Refer to the [Varbase documentation](https://docs.varbase.vardot.com/v/10.0.x/developers/theme-development-with-varbase)
+for more information on development.
+
+## Development
+
+### Install
+```sh
+yarn install
+yarn theme:init
+```
+
+### Watch
+```sh
+yarn theme:watch
+```
+
+### Build
+```sh
+yarn theme:full-build
+```
+
+## Deployment
+
+Commits to the `main` branch are [automatically deployed to production web server](https://github.com/BioData-PT/biodatapt-theme/actions/workflows/ssh-deploy.yml) using [GitHub Actions](https://github.com/features/actions).

biodatapt-theme/package.json

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+{
+ "name": "biodatapt",
+ "description": "A Drupal theme for the BioData.pt website based on Vartheme BS5.",
+ "private": true,
+ "engines": {
+ "npm": ">= 6.0",
+ "yarn": ">= 1.6",
+ "node": ">= 18.0"
+ },
+ "scripts": {
+ "theme:init": "webpack --progress --config webpack.config.init.js",
+ "theme:build": "webpack --progress --config webpack.config.build.js",
+ "theme:full-build": "yarn theme:build ; yarn components:build",
+ "theme:watch": "webpack --progress --config webpack.config.dev.js --watch",
+ "components:build": "webpack --progress --config webpack.config.components.js",
+ "phpcs": "phpcs --standard=./.phpcs.xml .",
+ "phpcbf": "phpcbf --standard=./.phpcs.xml .",
+ "lint:js": "node ./node_modules/eslint/bin/eslint.js .",
+ "lint:css": "stylelint \"**/*.css\"",
+ "lint:yaml": "node ./node_modules/eslint/bin/eslint.js --ext .yml ."
+ },
+ "license": "MIT",
+ "keywords": [
+ "drupal",
+ "webpack",
+ "bootstrap",
+ "BioData.pt",
+ "BioData.pt Theme",
+ "BioData.pt Theme (Bootstrap 5 - SASS)",
+ "frontend"
+ ],
+ "peerDependencies": {
+ "@popperjs/core": "^2.11.8"
+ },
+ "devDependencies": {
+ "bootstrap": "~5",
+ "bootstrap-icons": "~1",
+ "bootstrap-borders-utilities": "~1",
+ "bootstrap-ratio-utilities": "~1",
+ "@fortawesome/fontawesome-free": "~5",
+ "@popperjs/core": "~2",
+ "autoprefixer": "^10.4.17",
+ "@babel/core": "^7.23.9",
+ "@babel/preset-env": "^7.23.9",
+ "@babel/eslint-parser": "~7",
+ "babel-loader": "^8.2.2",
+ "clean-webpack-plugin": "^4.0.0",
+ "copy-webpack-plugin": "~11.0.0",
+ "core-js": "^3.9.1",
+ "css-loader": "^5.2.7",
+ "dotenv-safe": "^8.2.0",
+ "dotenv-webpack": "^7.0.1",
+ "es6-promise": "^4.1.1",
+ "eslint": "^8.56.0",
+ "eslint-config-xo": "^0.44.0",
+ "eslint-config-airbnb-base": "^15.0.0",
+ "eslint-config-prettier": "^8.4.0",
+ "eslint-import-resolver-webpack": "0.13.0",
+ "eslint-plugin-html": "^8.0.0",
+ "eslint-plugin-import": "^2.29.1",
+ "eslint-plugin-markdown": "^3.0.1",
+ "eslint-plugin-unicorn": "^51.0.1",
+ "eslint-plugin-jquery": "^1.5.1",
+ "eslint-plugin-jsx-a11y": "^6.2.3",
+ "eslint-plugin-prettier": "^4.0.0",
+ "eslint-plugin-yml": "^1.2.0",
+ "expose-loader": "^3.1.0",
+ "file-loader": "^5.0.2",
+ "glob": "^8.0.3",
+ "imagemin": "",
+ "img-loader": "^4.0.0",
+ "jquery": "~3.7.0",
+ "jquery-form": "4.3.x",
+ "jquery-ui": "1.13.x",
+ "js-cookie": "3.0.x",
+ "jsdom": "^20.0.0",
+ "loadjs": "4.2.x",
+ "mini-css-extract-plugin": "^0.11.3",
+ "minimist": "^1.2.2",
+ "mkdirp": "^1.0.4",
+ "nightwatch": "~3",
+ "normalize.css": "8.0.x",
+ "postcss": "^8.4.35",
+ "postcss-cli": "^11.0.0",
+ "postcss-header": "^3.0.2",
+ "postcss-import": "^15.0.0",
+ "postcss-loader": "^6.2.1",
+ "postcss-perfectionist": "^2.3.9",
+ "postcss-preset-env": "^8.3.2",
+ "postcss-pxtorem": "^6.0.0",
+ "postcss-rtlcss": "^3.5.2",
+ "postcss-url": "^10.1.3",
+ "prettier": "^2.1.2",
+ "raw-loader": "^4.0.2",
+ "sass": "^1.71.1",
+ "sass-true": "^7.0.1",
+ "sass-loader": "^12.3.0",
+ "sass-resources-loader": "^2.2.4",
+ "shepherd.js": "~10.0.1",
+ "sortablejs": "1.15.x",
+ "stylelint": "^16.2.1",
+ "stylelint-config-twbs-bootstrap": "^14.0.0",
+ "stylelint-checkstyle-formatter": "^0.1.2",
+ "stylelint-order": "^6.0.3",
+ "svg-inline-loader": "^0.8.2",
+ "svg-spritemap-webpack-plugin": "^4.4.0",
+ "tabbable": "~6.0.0",
+ "terser": "^5.27.2",
+ "terser-webpack-plugin": "^5.3.3",
+ "underscore": "~1.13.4",
+ "url-loader": "^4.1.1",
+ "webpack": "^5.77.0",
+ "webpack-cli": "^5.0.0",
+ "webpack-dev-middleware": "^4.1.0",
+ "webpack-merge": "^5.7.3",
+ "webpack-notifier": "^1.13.0",
+ "webpack-remove-empty-scripts": "^0.7.1"
+ },
+ "browserslist": [
+ "last 2 Chrome major versions",
+ "last 2 Firefox major versions",
+ "last 2 Safari major versions",
+ "last 2 Edge major versions",
+ "last 2 Opera versions",
+ "last 2 iOS major versions",
+ "last 1 ChromeAndroid version",
+ "last 1 Samsung version",
+ "Firefox ESR"
+ ]
+}

biodatapt-theme/scss/base/biodatapt.base.scss

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+@import '../defaults'; // Global defaults.
+
+// BioData.pt Base Global styling.
+// -----------------------------------------------------------------------------
+
+/* Temp fix for:
+ * Issue #3233533: Core .placeholder class conflicts with new Bootstrap .placeholder class
+ * https://www.drupal.org/project/drupal/issues/3233533
+ *
+ * Issue #3246827: Fix em.placeholder style from Bootstrap 5 base styling with the Drupal core placeholder
+ * https://www.drupal.org/i/3246827
+ */
+em.placeholder {
+ cursor: unset !important;
+ vertical-align: unset !important;
+ opacity: unset !important;
+ background-color: unset !important;
+}
+
+// Have a margin between field groups in forms.
+.form-group {
+ @include margin-bottom(1rem);
+}
+
+// Have a style form required fieldset, HTML input elements for fields.
+.form-required {
+ &::after {
+ content: '';
+ vertical-align: super;
+ display: inline-block;
+ background-image: url(../../images/required.svg);
+ background-repeat: no-repeat;
+ background-size: calc(#{$input-height} * 0.16666666666)
+ calc(#{$input-height} * 0.16666666666);
+ width: calc(#{$input-height} * 0.16666666666);
+ height: calc(#{$input-height} * 0.16666666666);
+ margin: 0 0.3em;
+ }
+}
+
+.ajax-progress {
+ background-color: transparent !important;
+ border: 0 !important;
+}
+
+.ajax-progress-throbber {
+ .throbber {
+ background-color: transparent !important;
+ border: 0 !important;
+ }
+
+ .message {
+ background-color: transparent !important;
+ border: 0 !important;
+ }
+}
+
+.ajax-progress-fullscreen {
+ background-color: transparent !important;
+}
+
+// Hide for anonymous users.
+.hidden-anonymous,
+.visible-admin,
+.visible-logged-in {
+ display: none !important;
+}
+
+// Show only for logged in users.
+body.user-logged-in {
+ .visible-admin,
+ .visible-logged-in,
+ .hidden-anonymous {
+ display: inline-block !important;
+ }
+
+ .btn {
+ .visible-admin,
+ .visible-logged-in,
+ .hidden-anonymous {
+ display: inline-block !important;
+ }
+ }
+}
+
+// Change Underline offset for inline links.
+a {
+ text-underline-offset: 0.25em;
+}
+
+// Custom BioData.pt styles
+
+h1,
+h2,
+h3,
+h4,
+h5,
+h6 {
+ font-family: 'Roboto Slab', sans-serif;
+}
+
+h1 {
+ text-transform: uppercase;
+ color: #f37021;
+}
+
+h3 {
+ text-transform: uppercase;
+ color: #662b14;
+ font-size: 1.17em;
+}
+
+// Show feed icon
+.feed-icon {
+ display: block;
+ overflow: hidden;
+ width: 16px;
+ height: 16px;
+ text-indent: -9999px;
+ background: url('/images/square-rss.svg') no-repeat;
+}
+
+// Fix navbar over Drupal admin elements:
+#page > nav {
+ z-index: 500;
+}
+
+// Job posting formatting
+.job-posting .field__label {
+ font-weight: bold;
+ margin-top: 1rem;
+}
+
+.field--name-schema-responsibilities .field__item::before {
+ content: '• ';
+}
+
+.field--name-schema-skills .field__item::before {
+ content: '• ';
+}
+
+// Logo size fix
+
+.navbar-brand img {
+ height: 55px;
+}
+
+@media (min-width: 1200px) {
+ .navbar-brand img {
+ height: 90px;
+ }
+}

biodatapt.info.yml

@@ -51,3 +51,4 @@ libraries-override:
 ckeditor_stylesheets: false
 ckeditor5-stylesheets: false
 enforce_prop_schemas: false
+

biodatapt.libraries.yml

@@ -199,3 +199,4 @@ bootstrap-icons:
  css:
  theme:
  fonts/bootstrap-icons/font/bootstrap-icons.min.css: { minified: true }
+

contrib/gin/.babelrc

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+{
+ "presets": [
+ [
+ "@babel/preset-env",
+ {
+ "useBuiltIns": "entry",
+ "corejs": "3"
+ }
+ ]
+ ]
+}

contrib/gin/.browserslistrc

@@ -0,0 +1,10 @@
+last 2 Chrome major versions
+last 2 Firefox major versions
+last 2 Safari major versions
+last 2 Edge major versions
+last 2 Opera versions
+last 2 iOS major versions
+last 1 ChromeAndroid version
+last 1 UCAndroid version
+last 1 Samsung version
+Firefox ESR