Merge branch 'develop'

README.md

@@ -40,11 +40,6 @@ pages. This is particularly useful for finding out whether newer posts on a part
 been made, as long as the author of the newer post remembered to link back to the older one. This
 feature acts like a bit like a "related posts" list on other websites.
 
-### Mathematical markup support
-ALP adds a TeX block to the Gutenberg editor in WordPress 5.0, allowing users to create equations.
-The equation is rendered within the editor so the user can check their markup, and the markup can be
-edited later alongside the rest of the post.
-
 ### Unread flags
 ALP tracks whether logged-in users have read new posts. When a new post is made, everyone except
 the post's author sees the new post as unread, designated in the *Labbook* theme using a closed
@@ -56,6 +51,12 @@ also click a link in the top bar to view a list of all unread posts.
 When a post undergoes significant edits, a post is again marked as unread to all users except the
 author.
 
+### Inventory system
+ALP adds an inventory system to allow you to create pages for inventory items. These pages can be
+used as a central place to store e.g. manuals, schematics, images, etc., and the system lets your
+users tag posts with inventory items which then provides links to these pages under the
+corresponding posts.
+
 ### Advanced search
 When used with the *Labbook* theme, ALP adds advanced search capabilities allowing users to
 search by categories, tags, coauthors, dates, and keywords. Users can also disallow posts made by
@@ -74,9 +75,18 @@ searches.
 Note: images are still accessible when the direct link is known - this is a shortcoming in WordPress
 itself. This can in most cases be mitigated with appropriate HTTP server configuration.
 
+### Mathematical markup support
+ALP adds a TeX block to the Gutenberg editor in WordPress 5.0, allowing users to create equations.
+The equation is rendered within the editor so the user can check their markup, and the markup can be
+edited later alongside the rest of the post.
+
 ### Term management
 ALP adds the ability to merge tags and categories in bulk.
 
+### Post changes
+ALP prevents posts being published with the "Uncategorized" category if the author has specified
+another category. In such cases, the "Uncategorized" category is silently removed.
+
 ### Page changes
 ALP modifies pages to work more like wiki pages. When using the *Labbook* theme, authors and dates
 are removed from the title area, a breadcrumb trail is shown back to the home page, and there is
@@ -157,11 +167,10 @@ outdated browsers, and this project is not concerned about losing sales from use
 ## Design principles
  - **Clean code**: there's an awful lot of terribly written code in the WordPress ecosystem. This
    plugin attempts to conform to coding standards, and to interfere minimally with the default
-   WordPress behaviour where possible. For some of the more major features, like coauthors,
-   some quiet major modifications are required to core behaviour, which means that ALP may not be
-   compatible with certain other plugins.
- - **Modular**: most/all features can be enabled or disabled, and work independently from each
-   other.
+   WordPress behaviour where possible.
+ - **Modular**: most features can be enabled or disabled via the settings page, and work
+   independently from each other. The plugin can also be used without the corresponding theme,
+   though this hides a lot of the useful parts of the plugin from users.
 
 ## Future development plans
 The basic behaviour of ALP is already in place, but the plan is to keep adding useful features

ssl-alp/README.txt

@@ -4,7 +4,7 @@ Tags: logbook, coauthor, revisions, references, latex, tex, mathematics, wiki
 Requires at least: 5.1.0
 Tested up to: 5.2.0
 Requires PHP: 7.0.0
-Stable tag: 0.15.2
+Stable tag: 0.16.0
 License: GNU General Public License v3 or later
 License URI: LICENCE
 
@@ -15,7 +15,7 @@ more.
 == Description ==
 Please also visit [our website](https://alp.attackllama.com/)!
 
-Academic Labbook Plugin (ALP) provides a lightweight but powerful set of tools
+Academic Labbook Plugin (ALP) provides a powerful set of tools
 on top of core WordPress to allow researchers to write about their work,
 leveraging the powerful WordPress platform. With ALP, you can benefit from
 WordPress's post compositition, tagging and categorisation, media management and
@@ -46,6 +46,12 @@ account in order to access the content. Combined with WordPress's disable login
 setting, and perhaps an LDAP authentication plugin, access can be tightly
 controlled.
 
+An "Inventory" system is added which lets your users create pages for lab
+equipment such as electronics. These pages can be used in whatever way you wish,
+such as to store manuals, images, guides and background information. Posts can
+also be tagged with inventory, and links to the corresponding inventory pages
+are shown under the post.
+
 ALP provides a tool to convert user roles from the blog-centric WordPress
 defaults to one more suitable for an academic group. The primary role becomes
 "Researcher" instead of "Editor", allowing users with this role to create, edit
@@ -73,6 +79,27 @@ on the ALP website.
 
 == Changelog ==
 
+= 0.16.0 =
+ - Renamed taxonomy term names. This is a BREAKING change and requires some
+   custom queries to be run to update old terms. See the GitHub release notes
+   for details.
+ - Added inventory system.
+ - Changed post revisions widget to show only posts with line changes.
+ - Changed post revision widget to use transients instead of cache; default
+   update time set to 5 minutes.
+ - Added check to remove "Uncategorised" category from posts with at least one
+   other category.
+ - Added check to avoid referenced posts which cannot be read by user from
+   showing in the cross-references list.
+ - Simplified permission checks when editing custom taxonomy terms.
+ - Updated KaTeX to 0.10.2.
+ - Fixed bug with coauthors not being assigned to posts on sites with existing
+   posts.
+ - Fixed bug with unread posts list pagination.
+ - Added tool to detect pretty permalink status.
+ - Expanded admin documentation.
+ - Numerous minor bug fixes.
+
 = 0.15.2 =
  - Fixed bug with media type definitions where trailing spaces caused types not
    to be saved.

ssl-alp/alp.php

@@ -3,7 +3,7 @@
  * Plugin Name:  Academic Labbook
  * Plugin URI:   https://alp.attackllama.com/
  * Description:  Turn WordPress into a collaborative academic labbook.
- * Version:      0.15.2
+ * Version:      0.16.0
  * Author:       Sean Leavey
  * Author URI:   https://attackllama.com/
  * License:      GPL3
@@ -21,7 +21,7 @@
  * Current plugin version.
  */
 
-define( 'SSL_ALP_VERSION', '0.15.2' );
+define( 'SSL_ALP_VERSION', '0.16.0' );
 
 /**
  * Plugin name
@@ -48,6 +48,7 @@
 define( 'SSL_ALP_SITE_TOOLS_MENU_SLUG', 'ssl-alp-admin-tools' );
 define( 'SSL_ALP_POST_REVISIONS_MENU_SLUG', 'ssl-alp-admin-post-revisions' );
 define( 'SSL_ALP_PAGE_REVISIONS_MENU_SLUG', 'ssl-alp-admin-page-revisions' );
+define( 'SSL_ALP_INVENTORY_REVISIONS_MENU_SLUG', 'ssl-alp-admin-inventory-revisions' );
 define( 'SSL_ALP_APPLICATIONS_MENU_SLUG', 'ssl-alp-admin-applications' );
 
 /**
@@ -60,7 +61,11 @@
  * Default settings
  */
 
-define( 'SSL_ALP_KATEX_VERSION', '0.10.1' );
+// KaTeX version.
+define( 'SSL_ALP_KATEX_VERSION', '0.10.2' );
+
+// Recent revisions widget cache timeout.
+define( 'SSL_ALP_RECENT_REVISIONS_CACHE_TIMEOUT', 5 * 60 );
 
 /**
  * Code to run on plugin activation and deactivation.

ssl-alp/includes/class-ssl-alp-activator.php

@@ -119,6 +119,7 @@ private static function add_options() {
 		add_option( 'ssl_alp_require_login', true );
 		add_option( 'ssl_alp_enable_applications', false );
 		add_option( 'ssl_alp_disallow_public_advanced_search', true );
+		add_option( 'ssl_alp_enable_inventory', true );
 		add_option( 'ssl_alp_allow_multiple_authors', true );
 		add_option( 'ssl_alp_disable_post_trackbacks', true );
 		add_option( 'ssl_alp_enable_crossreferences', true );

ssl-alp/includes/class-ssl-alp-authenticate-applications-list-table.php

@@ -57,7 +57,7 @@ public function prepare_items() {
 		$orderby  = ( isset( $_GET['orderby'] ) ) ? wp_unslash( $_GET['orderby'] ) : 'last_used';
 		$order    = ( isset( $_GET['order'] ) ) ? wp_unslash( $_GET['order'] ) : 'desc';
 
-		if ( array_key_exists( $orderby, $this->get_sortable_columns() )) {
+		if ( array_key_exists( $orderby, $this->get_sortable_columns() ) ) {
 			// Sort columns.
 			$this->items = wp_list_sort( $this->items, $orderby, $order );
 		}
@@ -88,11 +88,11 @@ public function prepare_items() {
 	}
 
 	public function column_cb( $item ) {
-        return sprintf(
+		return sprintf(
 			'<input type="checkbox" name="ssl_alp_applications[]" value="%s" />',
 			$item['slug']
-        );
-    }
+		);
+	}
 
 	public function column_password( $item ) {
 		// Break password into chunks.
@@ -155,7 +155,7 @@ protected function handle_row_actions( $application, $column_name, $primary ) {
 		}
 
 		$actions = array(
-			'revoke' => $ssl_alp->auth->get_revoke_url( $application )
+			'revoke' => $ssl_alp->auth->get_revoke_url( $application ),
 		);
 
 		return $this->row_actions( $actions );

ssl-alp/includes/class-ssl-alp-authenticate.php

@@ -210,8 +210,8 @@ public function output_admin_applications_page() {
 
 		// Create array with unique slugs as keys.
 		foreach ( $this->get_user_applications() as $application ) {
-			$slug = $this->generate_application_slug( $application );
-			$application['slug'] = $slug;
+			$slug                  = $this->generate_application_slug( $application );
+			$application['slug']   = $slug;
 			$applications[ $slug ] = $application;
 		}
 
@@ -268,7 +268,7 @@ public function print_admin_notices() {
 		}
 
 		switch ( $_GET['message'] ) {
-			case  'ssl_alp_add_success':
+			case 'ssl_alp_add_success':
 				echo '<div class="notice notice-success is-dismissible">';
 				echo '<p>' . esc_html__( 'Application added.', 'ssl-alp' ) . '</p>';
 				echo '</div>';
@@ -308,7 +308,13 @@ public function get_revoke_url( $application ) {
 		return sprintf(
 			'<a href="%1$s" class="ssl-alp-application-revoke" aria-label="$2$s">%3$s</a>',
 			wp_nonce_url( "admin-post.php?&amp;action=ssl-alp-revoke-application&amp;ssl_alp_applications[]={$application['slug']}", 'ssl-alp-manage-applications', 'ssl_alp_manage_applications_nonce' ),
-			esc_attr( sprintf( __( 'Revoke &#8220;%s&#8221;', 'ssl-alp' ), $application['name'] ) ),
+			esc_attr(
+				sprintf(
+					/* translators: application name to revoke */
+					__( 'Revoke &#8220;%s&#8221;', 'ssl-alp' ),
+					$application['name']
+				)
+			),
 			esc_html__( 'Revoke', 'ssl-alp' )
 		);
 	}
@@ -551,7 +557,7 @@ public function authenticate_application( $input_user, $username, $password ) {
 	}
 
 	private function authenticate_application_password( $username, $password ) {
-		$user = get_user_by( 'login',  $username );
+		$user = get_user_by( 'login', $username );
 
 		if ( ! $user ) {
 			return false;