Changed version number to match Drupal release tag conventions

tripal_analysis/tripal_analysis.info

@@ -3,7 +3,7 @@ description = Supports the companalyses tables of Chado by providing pages for v
 core = 7.x
 project = tripal_analysis
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 configure = admin/tripal/chado/tripal_analysis/configuration
 
 dependencies[] = tripal_core

tripal_bulk_loader/tripal_bulk_loader.info

@@ -3,7 +3,7 @@ description = Supports the construction of templates for customizable uploading
 core = 7.x
 project = tripal_bulk_loader
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

tripal_contact/tripal_contact.info

@@ -3,7 +3,7 @@ description = Supports the contact tables of Chado by providing pages for viewin
 core = 7.x
 project = tripal_contact
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

tripal_core/tripal_core.info

@@ -3,7 +3,7 @@ description = Provides support for all Tripal modules and includes the Tripal AP
 core = 7.x
 project = tripal_core
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 configure = admin/tripal
 
 stylesheets[all][] = theme/css/tripal.css

tripal_cv/tripal_cv.info

@@ -3,7 +3,7 @@ description = Supports the Controlled Vocabulary (CV) tables of Chado by providi
 core = 7.x
 project = tripal_cv
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 configure = admin/tripal/chado/tripal_cv
 
 dependencies[] = tripal_core

tripal_db/tripal_db.info

@@ -3,7 +3,7 @@ description = Supports the database cross-reference tables of Chado by providing
 core = 7.x
 project = tripal_db
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 configure = admin/tripal/chado/tripal_db
 
 dependencies[] = tripal_core

tripal_example/README.txt

@@ -74,9 +74,10 @@ features, or publications associated with featurmaps, etc.).  These template
 files and any JavaScript, CSS or images needed to suppport them are all
 housed inside of a 'theme' directory with the following structure:
 [module dir]/theme
-[module dir]/theme/css      (for CSS files)
-[module dir]/theme/js       (for JS files)
-[module dir]/theme/images   (for images)
+[module dir]/theme/css       (for CSS files)
+[module dir]/theme/js        (for JS files)
+[module dir]/theme/images    (for images)
+[module dir]/theme/templates (for all Drupal template files)
 
 All Drupal hooks and functions related to theming of content should go in the
 file named:
@@ -86,21 +87,12 @@ The functions in that file will typically be functions which directly
 generate content for a page or "preprocess" hooks that prepare variables that
 are passed to templates.
 
-Template files are typically placed inside of directories named after the 
-Tripal node type to which the template adds content.  For example, the 
-tripal_pub module is responsible for interactions with the publication tables
-of Chado.  It provides it's own 'chado_pub' node type.  But it also adds 
-publication information on feature pages if there is an associated publication.
-Therefore, the tripal_pub/theme/chado_feature directory exists and 
-contains the templates responsible for adding content to the 'chado_feature' 
-node type !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
 Template files are named in the following way
-[module dir]/theme/[template dir]/[module name]_[function].tpl.php.
+[module dir]/theme/templates/[module name]_[function].tpl.php.
 
 Notice that templates have an underscore separating the [module name] from the
 [function].  Typically a period is used (as with include files) but for
-backwards compatibility the undescores are kept.
+backwards compatibility the undescores are kept.  
 
 API Files
 ---------

tripal_example/api/tripal_example.api.inc

@@ -1 +1,33 @@
 <?php
+
+/**
+ * @file
+ * Provides an application programming interface (API) for working the example module
+ */
+
+/**
+ * @defgroup tripal_example_api Example API
+ * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) for working with features
+ * @}
+ */
+ 
+// EXPLANATION: This file is used for housing any API function that your
+// module creates.  It is suggested you follow the naming style for Tripal 
+// API functions. Below are naming rules for Tripal API functions:
+//
+// 1) Prefix the function with 'chado_' for all insert, updates, delete or get
+//    function on a table in the chado schema.  Tripal should provide all of these 
+//    functions for tables that come with Chado.  But, you can use this prefix 
+//    for API functions on custom tables that your module may add.
+// 2) For all other functions prefix the function with your module name. So
+//    for this example module the prefix would be 'tripal_example_'
+// 3) A 'verb' should follow the function prefix indicating the action that
+//    the function performs. Commonly used verbs are 'get', 'insert', 'update'
+//    'associate', 'execute', etc.  An exception is for functions that
+//    test state rather than perform an action (e.g. does something exist).  
+//    For functions that test state use 'does' instead of a verb 
+//    (e.g. tripal_example_does_pub_exist) 
+// 4) Follow the verb with a short predicate describing what is being acted upon.
+//

tripal_example/tripal_example.info

@@ -26,7 +26,7 @@ package = Tripal Extensions
 ; Follow these instructions when specifying the version:
 ; https:;drupal.org/node/1015226
 ; 
-version = 7.x-2.0
+version = 7.x-2.0.1-alpha
 
 ;
 ; Stylesheets containing CSS that should always be available for the

tripal_feature/tripal_feature.info

@@ -3,7 +3,7 @@ description = Supports the sequence (feature) tables of Chado by providing pages
 core = 7.x
 project = tripal_feature
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 
 stylesheets[all][] = theme/css/tripal_feature.css
 scripts[]          = theme/js/tripal_feature.js

tripal_featuremap/tripal_featuremap.info

@@ -3,7 +3,7 @@ description = Supports the map tables of Chado by providing pages for viewing an
 core = 7.x
 project = tripal_featuremap
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

tripal_genetic/tripal_genetic.info

@@ -3,7 +3,7 @@ description = Supports the genetic tables of Chado by providing pages for viewin
 core = 7.x
 project = tripal_genetic
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

tripal_library/tripal_library.info

@@ -3,7 +3,7 @@ description = Supports the library tables of Chado by providing pages for viewin
 core = 7.x
 project = tripal_library
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

tripal_natural_diversity/tripal_natural_diversity.info

@@ -3,7 +3,7 @@ description = Supports the natural diversity (ND) tables of Chado by providing p
 core = 7.x
 project = tripal_natural_diversity
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

tripal_organism/tripal_organism.info

@@ -3,7 +3,7 @@ description = Supports the organism tables of Chado by providing pages for viewi
 core = 7.x
 project = tripal_organism
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 configure = admin/tripal/chado/tripal_organism
 
 stylesheets[all][] = theme/css/tripal_organism.css

tripal_phenotype/tripal_phenotype.info

@@ -3,7 +3,7 @@ description = Supports the phenotype tables of Chado by providing pages for view
 core = 7.x
 project = tripal_phenotype
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

tripal_project/tripal_project.info

@@ -3,7 +3,7 @@ description = Supports the project tables of Chado by providing pages for viewin
 core = 7.x
 project = tripal_project
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 configure = admin/tripal/chado/tripal_project
 
 dependencies[] = tripal_core

tripal_pub/tripal_pub.info

@@ -3,7 +3,7 @@ description = Supports the pub (publication) tables of Chado by providing pages
 core = 7.x
 project = tripal_pub
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 
 stylesheets[all][] = theme/css/tripal_pub.css
 

tripal_stock/tripal_stock.info

@@ -3,7 +3,7 @@ description = Supports the stock tables of Chado by providing pages for viewing,
 core = 7.x
 project = tripal_stock
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

tripal_views/tripal_views.info

@@ -3,7 +3,7 @@ description = Integrates all Chado tables with Drupal Views and provides basic s
 core = 7.x
 project = tripal_core
 package = Tripal
-version = 7.x-2.0.1a
+version = 7.x-2.0.1-alpha
 configure = admin/tripal/views-integration
 
 files[] = views/handlers/tripal_views_handler_filter_textarea.inc