galaxyproject · jmchilton · Jun 15, 2016 · May 26, 2016 · May 26, 2016 · May 25, 2016
diff --git a/docs/_writing_cwl_intro.rst b/docs/_writing_cwl_intro.rst
@@ -64,6 +64,7 @@ tool is generated.
                         --example_input 2.fastq \
                         --example_output 2.fasta \
                         --container 'dukegcb/seqtk' \
+                        --test_case \
                         --help_from_command 'seqtk seq'
 
 This command generates the following CWL YAML file.
@@ -88,9 +89,49 @@ This command generates the following CWL YAML file.
     Applying linter new_draft... CHECK
     .. INFO: Modern CWL version [cwl:draft-3]
 
-A later revision of this document ill discuss defining more
-parameters for this tool and include information on generating and
-running tests with planemo for CWL tools.
+In addition to the actual tool file, a test file will be generated
+using the example command and provided test data. The file contents are as
+follows:
+
+.. literalinclude:: writing/seqtk_seq_tests_v3.yml
+   :language: yaml
+
+This file is a planemo-specific artifact. This file may contain 1 or more
+tests - each test is an element of the top-level list. ``tool_init`` will use
+the example command to build just one test.
+
+Each test consists of a few parts:
+
+- ``doc`` - this attribute provides a short description for the test.
+- ``job`` - this can be the path to a CWL job description or a job 
+  description embedded right in the test (``tool_init`` builds the latter). 
+- ``outputs`` - this section describes the expected output for a test. Each
+  output ID of the tool or workflow under test can appear as a key. The
+  example above just describes expected specific output file contents exactly
+  but many more expectations can be described.
+
+The tests described in this file can be run using the planemo ``test`` (or
+simply ``t``) command on the original file. By default, planemo will run tool
+tests with Galaxy but we can also specify the use of ``cwltool`` (the 
+reference implementation of CWL) which will be quicker and more robust until
+while Galaxy support for the CWL is still in development.
+
+    $ planemo test --no-container --engine cwltool seqtk_seq.cwl
+    Enable beta testing mode to test artifact that isn't a Galaxy tool.
+    All 1 test(s) executed passed.
+    seqtk_seq_0: passed
+
+We can also open up the Galaxy web inteface with this tool loaded
+using the ``serve`` (or just ``s``) command.
+
+::
+
+    $ planemo s --cwl seqtk_seq.cwl
+    ...
+    serving on http://127.0.0.1:9090
+
+Open up http://127.0.0.1:9090 in a web browser to view your new 
+tool.
 
 For more information on the Common Workflow Language check out the Draft 3
 `User Guide`_ and Specification_.

diff --git a/docs/_writing_test_and_serve.rst b/docs/_writing_test_and_serve.rst
@@ -1,7 +1,7 @@
 
 ::
 
-    $ planemo t --galaxy_root=/path/to/galaxy
+    $ planemo t
     ...
     All 1 test(s) executed passed.
     seqtk_seq[0]: passed
@@ -10,8 +10,12 @@ Now we can open Galaxy with the ``serve`` (or just ``s``).
 
 ::
 
-    $ planemo s --galaxy_root=/path/to/galaxy
+    $ planemo s
     ...
     serving on http://127.0.0.1:9090
 
 Open up http://127.0.0.1:9090 in a web browser to view your new tool.
+
+Serve and test can be passed various command line arguments such as
+``--galaxy_root`` to specify a Galaxy instance to use (by default 
+planemo will download and manage a instance just for planemo).
diff --git a/docs/galaxy_changelog.html b/docs/galaxy_changelog.html
@@ -3,18 +3,7 @@
   <head>
     <title>Galaxy Tool Framework Changes</title>
     <meta charset="utf-8">
-    <style>
-      @import url(https://fonts.googleapis.com/css?family=Yanone+Kaffeesatz);
-      @import url(https://fonts.googleapis.com/css?family=Droid+Serif:400,700,400italic);
-      @import url(https://fonts.googleapis.com/css?family=Ubuntu+Mono:400,700,400italic);
-
-      body { font-family: 'Droid Serif'; }
-      h1, h2, h3 {
-        font-family: 'Yanone Kaffeesatz';
-        font-weight: normal;
-      }
-      .remark-code, .remark-inline-code { font-family: 'Ubuntu Mono'; }
-    </style>
+    <link rel="stylesheet" type="text/css" href="style.css">
   </head>
   <body>
     <textarea id="source">

diff --git a/docs/images/organic_mower_wat.jpg b/docs/images/organic_mower_wat.jpg
diff --git a/docs/planemo.linters.rst b/docs/planemo.linters.rst
@@ -4,6 +4,14 @@ planemo.linters package
 Submodules
 ----------
 
+planemo.linters.doi module
+--------------------------
+
+.. automodule:: planemo.linters.doi
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 planemo.linters.urls module
 ---------------------------
 

diff --git a/docs/planemo.rst b/docs/planemo.rst
@@ -53,6 +53,14 @@ planemo.config module
     :undoc-members:
     :show-inheritance:
 
+planemo.docker module
+---------------------
+
+.. automodule:: planemo.docker
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 planemo.exit_codes module
 -------------------------
 

diff --git a/docs/planemo.test.rst b/docs/planemo.test.rst
@@ -4,6 +4,22 @@ planemo.test package
 Submodules
 ----------
 
+planemo.test.check_output module
+--------------------------------
+
+.. automodule:: planemo.test.check_output
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+planemo.test.data module
+------------------------
+
+.. automodule:: planemo.test.data
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 planemo.test.results module
 ---------------------------
 

diff --git a/docs/presentations/2016_workflows.html b/docs/presentations/2016_workflows.html
@@ -3,25 +3,20 @@
   <head>
     <title>Planemo: A Scientific Workflow SDK</title>
     <meta charset="utf-8">
-    <style>
-      @import url(https://fonts.googleapis.com/css?family=Yanone+Kaffeesatz);
-      @import url(https://fonts.googleapis.com/css?family=Droid+Serif:400,700,400italic);
-      @import url(https://fonts.googleapis.com/css?family=Ubuntu+Mono:400,700,400italic);
-
-      body { font-family: 'Droid Serif'; }
-      h1, h2, h3 {
-        font-family: 'Yanone Kaffeesatz';
-        font-weight: normal;
-      }
-      .remark-code, .remark-inline-code { font-family: 'Ubuntu Mono'; }
-    </style>
+    <link rel="stylesheet" type="text/css" href="style.css">
   </head>
   <body>
     <textarea id="source">
 
 class: center, middle
 
-## Planemo: A Scientific Workflow SDK
+layout: true
+class: inverse, middle
+
+---
+class: special
+# Planemo: A Scientific Workflow SDK
+John Chilton, Aysam Guerler, and the Galaxy Team
 
 ---
 
@@ -52,6 +47,9 @@
 
 ???
 
+The editor form now uses the same backbone driven MVC components as the
+new tool form presented last year.
+
 ---
 
 ### GUI Enhancements - Workflow Run Form
@@ -62,6 +60,84 @@
 
 ???
 
+The run workflow form has likewise been overhauled and will be merged soon. This
+should allow more dynamic option control when running workflows.
+
+---
+
+### GUI Enhancements - Labels
+
+TODO: UPDATE IMAGE
+
+![Workflow Run Form](images/gx_new_workflow_run.png)
+
+???
+
+When reasoning about workflows and connections between steps, persistent and unique 
+labels for steps and outputs are important. These are useful in the API and too a 
+lesser extent in the GUI today.
+
+A major theme of this presentation is going to be that workflows are programs, they
+are a coding artifact. I'm not sure anyone would disagree with me on that - but I 
+think the implications may be counter-intuitive at times.
+
+---
+
+### GUI Enhancements - Nested Workflows
+
+TODO: UPDATE IMAGE
+
+![Nested Workflows](images/gx_new_workflow_run.png)
+
+???
+
+Workflows are programs, languages describing programs should provide abstractions for
+composition. Nesting workflows was one of the most requested feature requests of 
+Galaxy and it now supports this.
+
+---
+
+### What About Planemo?
+
+???
+
+Enough screenshots right - when I present people expect to see long command-lines!
+
+---
+
+### Planemo's Success
+
+It is *the way* to develop Galaxy tools in 2016! Why?
+
+- Artifact-centric - not Galaxy-centric or registry-centric.
+- Fits into existing developer workflows - CLI, Git(hub), CI (Travis).
+- Flexible
+- Well documented w/focus on usage examples.
+
+It is about **developer workflow**.
+
+???
+
+In 2014, Greg von Kuster presented a tool development workflow that involved 
+publishing things to a local tool shed and running tests from there and viewing
+the results through the web interface. I call this registry or shed centric tool
+development (development activities "boot strap the tool shed, upload to the tool 
+shed, run tests against the tool shed, view results in the tool shed, export capsule
+from the tool shed". Prior to that tool development was Galaxy-centric - "download 
+Galaxy, update the Galaxy tool conf, update the Galaxy test data, run the Galaxy 
+tests." Planemo is tool centric - lint the tool, test the tool, serve the tool.
+
+---
+
+class: bottom
+background-image: url(images/organic_mower_wat.jpg)
+background-position: center;
+background-repeat: no-repeat;
+background-size: contain;
+
+### So Planemo?
+
+Photo Credit: Peter Smith (@skwiot)
 
 ---
 
@@ -75,8 +151,9 @@
 
 ???
 
-The artisinal, free range, organic text editor of my choice. It is a go 
-lang rewrite of a node rewrite of an Erlang editor from 1987 - it is the hottest editor you've never heard of.
+The hippest, artisinal, free range text editor of my choice. It is a go 
+lang rewrite of a node rewrite of an Erlang editor from 1987 - it is super hot right
+now but I'm sure you've never heard of.
 
 ---
 
@@ -90,17 +167,24 @@
 \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
 ```
 
-Neither human writable, nor human readable.
-
-JSON doesn't allow comments - one shouldn't have to describe a
-configuration file in JSON let alone write a program in it.
+- Neither human writable, nor human readable.
+- JSON doesn't allow comments.
+  - One shouldn't have to describe a configuration file in JSON,
+    let alone write a program in it.
 
 ---
 
-### Format 2 Workflows
+### Format 2 Workflows - Example
 
 TODO: SHOW EXAMPLE
 
+---
+
+### Format 2 Workflows
+
+- Started as a way to build test workflows for Galaxy testing framework.
+- All steps can be labeled, connections described by ID.
+- 
 
     </textarea>
     <script src="https://gnab.github.io/remark/downloads/remark-latest.min.js">