Generated gh-pages for commit 29117ee

Author: Camille Scott <[email protected]> bump version to 0.3
dib-lab · Apr 20, 2016 · bb987a5 · bb987a5
1 parent 29117ee
commit bb987a5
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Showing 29 changed files with 169 additions and 97 deletions.
diff --git a/doc/_build/doctrees/dammit.doctree b/doc/_build/doctrees/dammit.doctree
diff --git a/doc/_build/doctrees/environment.pickle b/doc/_build/doctrees/environment.pickle
diff --git a/doc/_build/doctrees/installing.doctree b/doc/_build/doctrees/installing.doctree
diff --git a/doc/_build/doctrees/usage.doctree b/doc/_build/doctrees/usage.doctree
diff --git a/doc/_build/html/.buildinfo b/doc/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 64826d1c217b464f7f30b0f247d41824
+config: 032ce66902ea756bbb2a97f4e0eb8c5c
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/_build/html/_modules/dammit/annotate.html b/doc/_build/html/_modules/dammit/annotate.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>dammit.annotate &mdash; dammit 0.2.9 documentation</title>
+    <title>dammit.annotate &mdash; dammit 0.3 documentation</title>
 
     <link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.2.9',
+        VERSION:     '0.3',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -26,7 +26,7 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="author" title="About these documents" href="../../about.html" />
-    <link rel="top" title="dammit 0.2.9 documentation" href="../../index.html" />
+    <link rel="top" title="dammit 0.3 documentation" href="../../index.html" />
     <link rel="up" title="Module code" href="../index.html" />
 
 
@@ -220,7 +220,8 @@ <h1>Source code for dammit.annotate</h1><div class="highlight"><pre>
                                <span class="bp">self</span><span class="o">.</span><span class="n">database_dict</span><span class="p">[</span><span class="s">&#39;PFAM&#39;</span><span class="p">],</span> 
                                <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">evalue</span><span class="p">,</span>
                                <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">n_threads</span><span class="p">,</span> 
-                               <span class="n">common</span><span class="o">.</span><span class="n">CONFIG</span><span class="p">[</span><span class="s">&#39;settings&#39;</span><span class="p">][</span><span class="s">&#39;hmmer&#39;</span><span class="p">][</span><span class="s">&#39;hmmscan&#39;</span><span class="p">])</span>
+                               <span class="n">common</span><span class="o">.</span><span class="n">CONFIG</span><span class="p">[</span><span class="s">&#39;settings&#39;</span><span class="p">][</span><span class="s">&#39;hmmer&#39;</span><span class="p">][</span><span class="s">&#39;hmmscan&#39;</span><span class="p">],</span>
+                               <span class="n">n_nodes</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">n_nodes</span><span class="p">)</span>
 
         <span class="k">yield</span> <span class="n">get_remap_hmmer_task</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">transdecoder_pfam_fn</span><span class="p">,</span>
                                    <span class="bp">self</span><span class="o">.</span><span class="n">transdecoder_orf_gff3_fn</span><span class="p">,</span>
@@ -243,7 +244,8 @@ <h1>Source code for dammit.annotate</h1><div class="highlight"><pre>
                                <span class="bp">self</span><span class="o">.</span><span class="n">database_dict</span><span class="p">[</span><span class="s">&#39;RFAM&#39;</span><span class="p">],</span> 
                                <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">evalue</span><span class="p">,</span>
                                <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">n_threads</span><span class="p">,</span> 
-                               <span class="n">cmscan_cfg</span><span class="p">)</span>
+                               <span class="n">cmscan_cfg</span><span class="p">,</span>
+                               <span class="n">n_nodes</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">n_nodes</span><span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">orthodb_task</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&#39;&#39;&#39;Run LAST to get homologies with OrthoDB. We use LAST here because</span>
@@ -258,7 +260,8 @@ <h1>Source code for dammit.annotate</h1><div class="highlight"><pre>
                                <span class="n">lastal_cfg</span><span class="p">,</span>
                                <span class="n">translate</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
                                <span class="n">cutoff</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">evalue</span><span class="p">,</span>
-                               <span class="n">n_threads</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">n_threads</span><span class="p">)</span>
+                               <span class="n">n_threads</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">n_threads</span><span class="p">,</span>
+                               <span class="n">n_nodes</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">n_nodes</span><span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">uniref_task</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 

diff --git a/doc/_build/html/_modules/dammit/blast.html b/doc/_build/html/_modules/dammit/blast.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>dammit.blast &mdash; dammit 0.2.9 documentation</title>
+    <title>dammit.blast &mdash; dammit 0.3 documentation</title>
 
     <link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.2.9',
+        VERSION:     '0.3',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -26,7 +26,7 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="author" title="About these documents" href="../../about.html" />
-    <link rel="top" title="dammit 0.2.9 documentation" href="../../index.html" />
+    <link rel="top" title="dammit 0.3 documentation" href="../../index.html" />
     <link rel="up" title="Module code" href="../index.html" />
 
 

diff --git a/doc/_build/html/_modules/dammit/common.html b/doc/_build/html/_modules/dammit/common.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>dammit.common &mdash; dammit 0.2.9 documentation</title>
+    <title>dammit.common &mdash; dammit 0.3 documentation</title>
 
     <link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.2.9',
+        VERSION:     '0.3',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -26,7 +26,7 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="author" title="About these documents" href="../../about.html" />
-    <link rel="top" title="dammit 0.2.9 documentation" href="../../index.html" />
+    <link rel="top" title="dammit 0.3 documentation" href="../../index.html" />
     <link rel="up" title="Module code" href="../index.html" />
 
 

diff --git a/doc/_build/html/_modules/dammit/databases.html b/doc/_build/html/_modules/dammit/databases.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>dammit.databases &mdash; dammit 0.2.9 documentation</title>
+    <title>dammit.databases &mdash; dammit 0.3 documentation</title>
 
     <link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.2.9',
+        VERSION:     '0.3',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -26,7 +26,7 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="author" title="About these documents" href="../../about.html" />
-    <link rel="top" title="dammit 0.2.9 documentation" href="../../index.html" />
+    <link rel="top" title="dammit 0.3 documentation" href="../../index.html" />
     <link rel="up" title="Module code" href="../index.html" />
 
 

diff --git a/doc/_build/html/_modules/dammit/dependencies.html b/doc/_build/html/_modules/dammit/dependencies.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>dammit.dependencies &mdash; dammit 0.2.9 documentation</title>
+    <title>dammit.dependencies &mdash; dammit 0.3 documentation</title>
 
     <link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.2.9',
+        VERSION:     '0.3',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -26,7 +26,7 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="author" title="About these documents" href="../../about.html" />
-    <link rel="top" title="dammit 0.2.9 documentation" href="../../index.html" />
+    <link rel="top" title="dammit 0.3 documentation" href="../../index.html" />
     <link rel="up" title="Module code" href="../index.html" />
 
 

diff --git a/doc/_build/html/_modules/dammit/gff.html b/doc/_build/html/_modules/dammit/gff.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>dammit.gff &mdash; dammit 0.2.9 documentation</title>
+    <title>dammit.gff &mdash; dammit 0.3 documentation</title>
 
     <link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.2.9',
+        VERSION:     '0.3',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -26,7 +26,7 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="author" title="About these documents" href="../../about.html" />
-    <link rel="top" title="dammit 0.2.9 documentation" href="../../index.html" />
+    <link rel="top" title="dammit 0.3 documentation" href="../../index.html" />
     <link rel="up" title="Module code" href="../index.html" />
 
 

diff --git a/doc/_build/html/_modules/dammit/parsers.html b/doc/_build/html/_modules/dammit/parsers.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>dammit.parsers &mdash; dammit 0.2.9 documentation</title>
+    <title>dammit.parsers &mdash; dammit 0.3 documentation</title>
 
     <link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.2.9',
+        VERSION:     '0.3',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -26,7 +26,7 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="author" title="About these documents" href="../../about.html" />
-    <link rel="top" title="dammit 0.2.9 documentation" href="../../index.html" />
+    <link rel="top" title="dammit 0.3 documentation" href="../../index.html" />
     <link rel="up" title="Module code" href="../index.html" />
 
 

diff --git a/doc/_build/html/_modules/dammit/report.html b/doc/_build/html/_modules/dammit/report.html
@@ -6,7 +6,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>dammit.report &mdash; dammit 0.2.9 documentation</title>
+    <title>dammit.report &mdash; dammit 0.3 documentation</title>
 
     <link rel="stylesheet" href="../../_static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    '../../',
-        VERSION:     '0.2.9',
+        VERSION:     '0.3',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -26,7 +26,7 @@
     <script type="text/javascript" src="../../_static/doctools.js"></script>
     <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="author" title="About these documents" href="../../about.html" />
-    <link rel="top" title="dammit 0.2.9 documentation" href="../../index.html" />
+    <link rel="top" title="dammit 0.3 documentation" href="../../index.html" />
     <link rel="up" title="Module code" href="../index.html" />