Deploying to gh-pages from @ 20af039 🚀

api/engine.html

@@ -190,7 +190,7 @@ <h4><a class="reference internal" href="#capsul.engine.activate_configuration" t
 configuration modules, which provide additional configuration variables,
 and “environments” which typically represent computing resources.</p>
 <p><em>Computing resources</em></p>
-<p>Capsul is using <a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a> to run
+<p>Capsul is using <a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a> to run
 processes, and is thus able to connect and execute on a remote computing
 server. The remote computing resource may have a different configuration
 from the client one (paths for software or data, available external

api/pipeline.html

@@ -1498,7 +1498,7 @@ <h4><a class="reference internal" href="#capsul.pipeline.pipeline_nodes.Optional
 <dt class="sig sig-object py" id="capsul.pipeline.pipeline_nodes.Node.is_job">
 <span class="sig-name descname"><span class="pre">is_job</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/capsul/pipeline/pipeline_nodes.html#Node.is_job"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#capsul.pipeline.pipeline_nodes.Node.is_job" title="Link to this definition">¶</a></dt>
 <dd><p>if True, the node will be represented as a Job in
-<a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a>. Otherwise the node is static
+<a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a>. Otherwise the node is static
 and does not run.</p>
 </dd></dl>
 
@@ -1845,7 +1845,7 @@ <h4><a class="reference internal" href="#capsul.pipeline.pipeline_nodes.Optional
 <dt class="sig sig-object py" id="capsul.pipeline.pipeline_nodes.ProcessNode.is_job">
 <span class="sig-name descname"><span class="pre">is_job</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/capsul/pipeline/pipeline_nodes.html#ProcessNode.is_job"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#capsul.pipeline.pipeline_nodes.ProcessNode.is_job" title="Link to this definition">¶</a></dt>
 <dd><p>if True, the node will be represented as a Job in
-<a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a>. Otherwise the node is static
+<a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a>. Otherwise the node is static
 and does not run.</p>
 </dd></dl>
 
@@ -2073,7 +2073,7 @@ <h4><a class="reference internal" href="#capsul.pipeline.pipeline_nodes.Optional
 <dt class="sig sig-object py" id="capsul.pipeline.pipeline_nodes.Switch.is_job">
 <span class="sig-name descname"><span class="pre">is_job</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/capsul/pipeline/pipeline_nodes.html#Switch.is_job"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#capsul.pipeline.pipeline_nodes.Switch.is_job" title="Link to this definition">¶</a></dt>
 <dd><p>if True, the node will be represented as a Job in
-<a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a>. Otherwise the node is static
+<a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a>. Otherwise the node is static
 and does not run.</p>
 </dd></dl>
 
@@ -3162,7 +3162,7 @@ <h4><a class="reference internal" href="#capsul.pipeline.custom_nodes.strconv.St
 <dt class="sig sig-object py" id="capsul.pipeline.custom_nodes.strconv.StrConvNode.is_job">
 <span class="sig-name descname"><span class="pre">is_job</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/capsul/pipeline/custom_nodes/strconv.html#StrConvNode.is_job"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#capsul.pipeline.custom_nodes.strconv.StrConvNode.is_job" title="Link to this definition">¶</a></dt>
 <dd><p>if True, the node will be represented as a Job in
-<a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a>. Otherwise the node is static
+<a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a>. Otherwise the node is static
 and does not run.</p>
 </dd></dl>
 

api/process.html

@@ -416,7 +416,7 @@ <h4><a class="reference internal" href="#capsul.process.process.ProcessResult" t
 <p>A process is typically an object with typed parameters, and an execution
 function. Parameters are described using Enthought
 <a class="reference external" href="http://docs.enthought.com/traits/">traits</a> through Soma-Base
-<a class="reference external" href="http://brainvisa.info/soma-base/sphinx/api.html#soma.controller.controller.Controller">Controller</a>
+<a class="reference external" href="https://brainvisa.info/soma-base/sphinx/api.html#soma.controller.controller.Controller">Controller</a>
 base class.</p>
 <p>In addition to describing its parameters, a Process must implement its
 execution function, either through a python method, by overloading

api/study_config.html

@@ -1446,11 +1446,11 @@ <h4><a class="reference internal" href="#capsul.study_config.config_modules.soma
 <dl class="py class">
 <dt class="sig sig-object py" id="capsul.study_config.config_modules.somaworkflow_config.SomaWorkflowConfig">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">capsul.study_config.config_modules.somaworkflow_config.</span></span><span class="sig-name descname"><span class="pre">SomaWorkflowConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">study_config</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/capsul/study_config/config_modules/somaworkflow_config.html#SomaWorkflowConfig"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#capsul.study_config.config_modules.somaworkflow_config.SomaWorkflowConfig" title="Link to this definition">¶</a></dt>
-<dd><p>Configuration module for <a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a></p>
+<dd><p>Configuration module for <a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/index.html">Soma-Workflow</a></p>
 <p>Stores configuration options which are not part of Soma-Workflow own
 configuration, and used to run workflows from CAPSUL pipelines.</p>
 <p>The configuration module may also store connected Soma-Workflow
-<a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/client_API.html">WorkflowController</a> objects to allow
+<a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/client_API.html">WorkflowController</a> objects to allow
 monitoring and submitting workflows.</p>
 <dl class="py attribute">
 <dt class="sig sig-object py" id="capsul.study_config.config_modules.somaworkflow_config.SomaWorkflowConfig.use_soma_workflow">
@@ -1563,7 +1563,7 @@ <h4><a class="reference internal" href="#capsul.study_config.config_modules.soma
 </ul>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/client_API.html">WorkflowController</a> object</p>
+<dd class="field-even"><p><a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/client_API.html">WorkflowController</a> object</p>
 </dd>
 </dl>
 </dd></dl>
@@ -1572,7 +1572,7 @@ <h4><a class="reference internal" href="#capsul.study_config.config_modules.soma
 <dt class="sig sig-object py" id="id24">
 <span class="sig-name descname"><span class="pre">disconnect_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resource_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/capsul/study_config/config_modules/somaworkflow_config.html#SomaWorkflowConfig.disconnect_resource"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id24" title="Link to this definition">¶</a></dt>
 <dd><p>Disconnect a connected
-<a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/client_API.html">WorkflowController</a> and removes it
+<a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/client_API.html">WorkflowController</a> and removes it
 from the internal list</p>
 </dd></dl>
 
@@ -1601,7 +1601,7 @@ <h4><a class="reference internal" href="#capsul.study_config.config_modules.soma
 <dt class="sig sig-object py" id="id26">
 <span class="sig-name descname"><span class="pre">get_workflow_controller</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resource_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/capsul/study_config/config_modules/somaworkflow_config.html#SomaWorkflowConfig.get_workflow_controller"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id26" title="Link to this definition">¶</a></dt>
 <dd><p>Get a connected
-<a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/client_API.html">WorkflowController</a> for the given
+<a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/client_API.html">WorkflowController</a> for the given
 resource</p>
 </dd></dl>
 

index.html

@@ -127,7 +127,7 @@ <h3>Navigation</h3>
 
   <section id="capsul">
 <h1>CAPSUL<a class="headerlink" href="#capsul" title="Link to this heading">¶</a></h1>
-<p>Capsul is a free and open-source <a class="reference external" href="http://python.org">Python</a> library for encapsulating algorithms and chain them in pipelines. It has unique features for building and dealing with complex pipelines. It is designed to make it easy to execute pipelines in various environments ranging from a local computer to a remote computing center. Capsul is connected to <a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/index.html">soma-workflow</a> in order to manage all the difficulties of running a lot of pipelines in parallel.</p>
+<p>Capsul is a free and open-source <a class="reference external" href="http://python.org">Python</a> library for encapsulating algorithms and chain them in pipelines. It has unique features for building and dealing with complex pipelines. It is designed to make it easy to execute pipelines in various environments ranging from a local computer to a remote computing center. Capsul is connected to <a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/index.html">soma-workflow</a> in order to manage all the difficulties of running a lot of pipelines in parallel.</p>
 <ul class="simple">
 <li><p>doc of the current stable release: <a class="reference external" href="http://brainvisa.info/capsul/">http://brainvisa.info/capsul/</a></p></li>
 <li><p>sources on gitHub: <a class="reference external" href="https://github.com/populse/capsul">https://github.com/populse/capsul</a></p></li>
@@ -140,7 +140,7 @@ <h2>Main features<a class="headerlink" href="#main-features" title="Link to this
 <li><p>An iteration system allows to iterate runs, or pipeline nodes, over a set of parameters configurations.</p></li>
 <li><p>Capsul provides a GUI (graphical user interface) to display pipelines structure in a boxes and links representation, to enter parameters, to iterate runs… The GUI allows basic pipeline edition and graphical building.</p></li>
 <li><p>Pipelines can be saved as XML files. They can thus be written either as Python source files, or as XML files.</p></li>
-<li><p>Pipeline execution can optionally make use of <a class="reference external" href="http://brainvisa.info/soma-workflow/sphinx/index.html">soma-workflow</a>, which manages execution dependencies between pipeline nodes and can run in parallel independent ones, can run and monitor pipelines either locally or remotely on a distant computing resource (a cluster for instance).</p></li>
+<li><p>Pipeline execution can optionally make use of <a class="reference external" href="https://brainvisa.info/soma-workflow/sphinx/index.html">soma-workflow</a>, which manages execution dependencies between pipeline nodes and can run in parallel independent ones, can run and monitor pipelines either locally or remotely on a distant computing resource (a cluster for instance).</p></li>
 <li><p>Capsul has a compatibility with <a class="reference external" href="http://nipype.readthedocs.io/en/latest/">Nipype</a> interfaces which can be directly used as pipeline nodes.</p></li>
 </ul>
 </section>
@@ -149,7 +149,7 @@ <h2>Technical features<a class="headerlink" href="#technical-features" title="Li
 <ul class="simple">
 <li><p>Capsul is compatible with Python 2 (&gt;= 2.7) and Python 3 (&gt;= 3.4).</p></li>
 <li><p>The Gui is based on <a class="reference external" href="https://www.qt.io/developers/">Qt</a> and can use <a class="reference external" href="https://riverbankcomputing.com">PyQt4</a>, <a class="reference external" href="https://riverbankcomputing.com">PyQt5</a>, or <a class="reference external" href="https://wiki.qt.io/PySide">PySide</a>.</p></li>
-<li><p>Most dependencies are optional: Gui (Qt/PyQt), NiPype, and Soma-Workflow, can be disabled, with the main pipelining features still working. The only mandatory dependency is <a class="reference external" href="http://brainvisa.info/soma-base/sphinx/index.html">Soma-Base</a>, which is developed by the same team (at Neurospin) and can be regarded as an independent basis for Capsul.</p></li>
+<li><p>Most dependencies are optional: Gui (Qt/PyQt), NiPype, and Soma-Workflow, can be disabled, with the main pipelining features still working. The only mandatory dependency is <a class="reference external" href="https://brainvisa.info/soma-base/sphinx/index.html">Soma-Base</a>, which is developed by the same team (at Neurospin) and can be regarded as an independent basis for Capsul.</p></li>
 </ul>
 </section>
 <section id="documentation-contents">

tutorial/capsul_tutorial.html

@@ -1144,7 +1144,7 @@ <h1><p>StudyConfig</p>
 somaworkflow_config_file :   &lt;undefined&gt;
 somaworkflow_keep_failed_workflows :   True
 somaworkflow_keep_succeeded_workflows :   False
-somaworkflow_computing_resources_config :   &lt;soma.controller.controller.OpenKeyController object at 0x7fc5900bd1d0&gt;
+somaworkflow_computing_resources_config :   &lt;soma.controller.controller.OpenKeyController object at 0x7f81742f3d10&gt;
 spm_directory :   &lt;undefined&gt;
 spm_standalone :   &lt;undefined&gt;
 spm_version :   &lt;undefined&gt;
@@ -1303,8 +1303,8 @@ <h1><p>Distributed execution using Soma-Workflow</p>
 </div>
 <div class="output_area docutils container">
 <div class="highlight"><pre>
-jobs: [&lt;soma_workflow.client_types.Job object at 0x7fc588cb54c0&gt;, &lt;soma_workflow.client_types.Job object at 0x7fc588cb58b0&gt;]
-dependencies: {(&lt;soma_workflow.client_types.Job object at 0x7fc588cb58b0&gt;, &lt;soma_workflow.client_types.Job object at 0x7fc588cb54c0&gt;)}
+jobs: [&lt;soma_workflow.client_types.Job object at 0x7f816cf5a2b0&gt;, &lt;soma_workflow.client_types.Job object at 0x7f816cf5a130&gt;]
+dependencies: {(&lt;soma_workflow.client_types.Job object at 0x7f816cf5a130&gt;, &lt;soma_workflow.client_types.Job object at 0x7f816cf5a2b0&gt;)}
 </pre></div></div>
 </div>
 <p>The workwlow can be saved and reloaded in soma_workflow_gui, or used in a soma-workflow controller:</p>
@@ -1811,20 +1811,13 @@ <h2><p>File names completion using FOM</p>
 </pre></div>
 </div>
 </div>
-<div class="nboutput docutils container">
+<div class="nboutput nblast docutils container">
 <div class="prompt empty docutils container">
 </div>
 <div class="output_area docutils container">
 <div class="highlight"><pre>
 switch proc_select2 value: proc3
 output image_out5: /data/capsul_demo/subjects_irm2/out_image_irm2_3.nii.gz
-</pre></div></div>
-</div>
-<div class="nboutput nblast docutils container">
-<div class="prompt empty docutils container">
-</div>
-<div class="output_area docutils container">
-<div class="highlight"><pre>
 switch proc_select2 value: proc4
 output image_out5: /data/capsul_demo/subjects_irm2/out_image_irm2_4.nii.gz
 </pre></div></div>