Update documentation and HISTORY.rst for new release.

galaxyproject · Feb 13, 2015 · 07f4f6c · 07f4f6c
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -3,6 +3,23 @@
 History
 -------
 
+---------------------
+0.3.0 (2015-02-13)
+---------------------
+
+ * Add option (``-r``) to the ``shed_upload`` command to recursively upload
+   subdirectories (thanks to Eric Rasche). `Pull Request 68`_
+ * Fix diff formatting in test reports (thanks to Eric Rasche).
+   `Pull Request 63`_
+ * Grab updated test database to speed up testing (thanks to approach from
+   Eric Rasche and Dannon Baker). `Issue 61`_, dff4f33_
+ * Fix test data command-line argument name (was ``test-data`` now it is
+   ``test_data``). 834bfb2_
+ * Use ``tool_data_table_conf.xml.sample`` file if
+   ``tool_data_table_conf.xml.test`` is unavailable. Should allow some
+  new tools to be tested without modifying Galaxy's global
+  ``tool_data_table_conf.xml`` file. ac4f828_
+
 ---------------------
 0.2.0 (2015-01-13)
 ---------------------
@@ -52,6 +69,9 @@ History
 * Initial work on the project - commands for testing, linting, serving Galaxy
   tools - and more experimental features involving Docker and Homebrew. 7d07782_
 
+.. _Pull Request 68: https://github.com/galaxyproject/planemo/pull/68
+.. _Issue 61: https://github.com/galaxyproject/planemo/issues/61
+.. _Pull Request 63: https://github.com/galaxyproject/planemo/pull/63
 .. _Pull Request 56: https://github.com/galaxyproject/planemo/pull/56
 .. _Pull Request 51: https://github.com/galaxyproject/planemo/pull/51
 .. _Pull Request 40: https://github.com/galaxyproject/planemo/pull/40
@@ -61,6 +81,9 @@ History
 .. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33
 .. _Pull Request 6: https://github.com/galaxyproject/planemo/pull/6
 .. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1
+.. _ac4f828: https://github.com/galaxyproject/planemo/ac4f82898f7006799142503a33c3978428660ce7
+.. _834bfb2: https://github.com/galaxyproject/planemo/commit/834bfb2929d367892a3abe9c0b88d5a0277d7905
+.. _dff4f33: https://github.com/galaxyproject/planemo/commit/dff4f33c750a8dbe651c38e149a26dd42e706a82
 .. _a4110a8: https://github.com/galaxyproject/planemo/commit/a4110a85a770988e5cd3c31ccc9475717897d59c
 .. _21bb463: https://github.com/galaxyproject/planemo/commit/21bb463ad6c321bcb669603049a5e89a69766ad9
 .. _af39061: https://github.com/galaxyproject/planemo/commit/af390612004dab636d8696839bb723d39f97c85d

diff --git a/docs/commands/serve.rst b/docs/commands/serve.rst
@@ -36,7 +36,7 @@ instances.
                                       execute command with.
       --install_galaxy                Download and configure a disposable copy of
                                       Galaxy from github.
-      --test-data DIRECTORY           test-data directory to for specified
+      --test_data DIRECTORY           test-data directory to for specified
                                       tool(s).
       --dependency_resolvers_config_file PATH
                                       Dependency resolver configuration for Galaxy

diff --git a/docs/commands/shed_upload.rst b/docs/commands/shed_upload.rst
@@ -12,7 +12,7 @@ This section is auto-generated from the help text for the planemo command
 
 **Help**
 
-Upload a tool directory as a tarball to a tool shed.
+Handle possible recursion through paths for uploading files to a toolshed
 
 **Options**::
 
@@ -34,5 +34,7 @@ Upload a tool directory as a tarball to a tool shed.
                             tool shed.
       --tar PATH            Specify a pre-existing tar file instead of
                             automatically building one as part of this command.
+      -r, --recursive       Recursively search for repositories to publish to a
+                            tool shed
       --help                Show this message and exit.
     
diff --git a/docs/commands/test.rst b/docs/commands/test.rst
@@ -61,8 +61,10 @@ please careful and do not try this against production Galaxy instances.
                                       execute command with.
       --install_galaxy                Download and configure a disposable copy of
                                       Galaxy from github.
-      --test-data DIRECTORY           test-data directory to for specified
+      --test_data DIRECTORY           test-data directory to for specified
                                       tool(s).
+      --tool_data_table PATH          tool_data_table_conf.xml file to for
+                                      specified tool(s).
       --dependency_resolvers_config_file PATH
                                       Dependency resolver configuration for Galaxy
                                       to target.