I am changing clustergrammer module to clustergrammer_py, which build…

…s docs with updatable documentation and in a separate test worked in readthedocs.io
cornhundred · Feb 17, 2017 · f79e47b · f79e47b
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Showing 92 changed files with 213 additions and 350 deletions.
diff --git a/clustergrammer/__init__.pyc b/clustergrammer/__init__.pyc
diff --git a/clustergrammer/__init__.py → clustergrammer_py/__init__.py b/clustergrammer/__init__.py → clustergrammer_py/__init__.py
@@ -2,6 +2,9 @@
 class Network(object):
   '''
   version 1.2.1
+
+  Updating documentation
+
   Networks have two states:
 
   1) the data state, where they are stored as a matrix and nodes

diff --git a/clustergrammer_py/__init__.pyc b/clustergrammer_py/__init__.pyc
diff --git a/...ammer/__pycache__/__init__.cpython-35.pyc → ...er_py/__pycache__/__init__.cpython-35.pyc b/...ammer/__pycache__/__init__.cpython-35.pyc → ...er_py/__pycache__/__init__.cpython-35.pyc
diff --git a/...mer/__pycache__/calc_clust.cpython-35.pyc → ..._py/__pycache__/calc_clust.cpython-35.pyc b/...mer/__pycache__/calc_clust.cpython-35.pyc → ..._py/__pycache__/calc_clust.cpython-35.pyc
diff --git a/...ammer/__pycache__/cat_pval.cpython-35.pyc → ...er_py/__pycache__/cat_pval.cpython-35.pyc b/...ammer/__pycache__/cat_pval.cpython-35.pyc → ...er_py/__pycache__/cat_pval.cpython-35.pyc
diff --git a/...mer/__pycache__/categories.cpython-35.pyc → ..._py/__pycache__/categories.cpython-35.pyc b/...mer/__pycache__/categories.cpython-35.pyc → ..._py/__pycache__/categories.cpython-35.pyc
diff --git a/...r/__pycache__/data_formats.cpython-35.pyc → ...y/__pycache__/data_formats.cpython-35.pyc b/...r/__pycache__/data_formats.cpython-35.pyc → ...y/__pycache__/data_formats.cpython-35.pyc
diff --git a/...ycache__/enrichr_functions.cpython-35.pyc → ...ycache__/enrichr_functions.cpython-35.pyc b/...ycache__/enrichr_functions.cpython-35.pyc → ...ycache__/enrichr_functions.cpython-35.pyc
diff --git a/...er/__pycache__/export_data.cpython-35.pyc → ...py/__pycache__/export_data.cpython-35.pyc b/...er/__pycache__/export_data.cpython-35.pyc → ...py/__pycache__/export_data.cpython-35.pyc
diff --git a/...__pycache__/initialize_net.cpython-35.pyc → ...__pycache__/initialize_net.cpython-35.pyc b/...__pycache__/initialize_net.cpython-35.pyc → ...__pycache__/initialize_net.cpython-35.pyc
diff --git a/...mmer/__pycache__/load_data.cpython-35.pyc → ...r_py/__pycache__/load_data.cpython-35.pyc b/...mmer/__pycache__/load_data.cpython-35.pyc → ...r_py/__pycache__/load_data.cpython-35.pyc
diff --git a/...__pycache__/make_clust_fun.cpython-35.pyc → ...__pycache__/make_clust_fun.cpython-35.pyc b/...__pycache__/make_clust_fun.cpython-35.pyc → ...__pycache__/make_clust_fun.cpython-35.pyc
diff --git a/...r/__pycache__/make_sim_mat.cpython-35.pyc → ...y/__pycache__/make_sim_mat.cpython-35.pyc b/...r/__pycache__/make_sim_mat.cpython-35.pyc → ...y/__pycache__/make_sim_mat.cpython-35.pyc
diff --git a/...mer/__pycache__/make_views.cpython-35.pyc → ..._py/__pycache__/make_views.cpython-35.pyc b/...mer/__pycache__/make_views.cpython-35.pyc → ..._py/__pycache__/make_views.cpython-35.pyc
diff --git a/...ammer/__pycache__/make_viz.cpython-35.pyc → ...er_py/__pycache__/make_viz.cpython-35.pyc b/...ammer/__pycache__/make_viz.cpython-35.pyc → ...er_py/__pycache__/make_viz.cpython-35.pyc
diff --git a/...__pycache__/proc_df_labels.cpython-35.pyc → ...__pycache__/proc_df_labels.cpython-35.pyc b/...__pycache__/proc_df_labels.cpython-35.pyc → ...__pycache__/proc_df_labels.cpython-35.pyc
diff --git a/...mer/__pycache__/run_filter.cpython-35.pyc → ..._py/__pycache__/run_filter.cpython-35.pyc b/...mer/__pycache__/run_filter.cpython-35.pyc → ..._py/__pycache__/run_filter.cpython-35.pyc
diff --git a/clustergrammer/calc_clust.py → clustergrammer_py/calc_clust.py b/clustergrammer/calc_clust.py → clustergrammer_py/calc_clust.py
diff --git a/clustergrammer/calc_clust.pyc → clustergrammer_py/calc_clust.pyc b/clustergrammer/calc_clust.pyc → clustergrammer_py/calc_clust.pyc
diff --git a/clustergrammer/cat_pval.py → clustergrammer_py/cat_pval.py b/clustergrammer/cat_pval.py → clustergrammer_py/cat_pval.py
diff --git a/clustergrammer/cat_pval.pyc → clustergrammer_py/cat_pval.pyc b/clustergrammer/cat_pval.pyc → clustergrammer_py/cat_pval.pyc
diff --git a/clustergrammer/categories.py → clustergrammer_py/categories.py b/clustergrammer/categories.py → clustergrammer_py/categories.py
diff --git a/clustergrammer/categories.pyc → clustergrammer_py/categories.pyc b/clustergrammer/categories.pyc → clustergrammer_py/categories.pyc
diff --git a/clustergrammer/data_formats.py → clustergrammer_py/data_formats.py b/clustergrammer/data_formats.py → clustergrammer_py/data_formats.py
diff --git a/clustergrammer/data_formats.pyc → clustergrammer_py/data_formats.pyc b/clustergrammer/data_formats.pyc → clustergrammer_py/data_formats.pyc
diff --git a/clustergrammer/enrichr_functions.py → clustergrammer_py/enrichr_functions.py b/clustergrammer/enrichr_functions.py → clustergrammer_py/enrichr_functions.py
diff --git a/clustergrammer/enrichr_functions.pyc → clustergrammer_py/enrichr_functions.pyc b/clustergrammer/enrichr_functions.pyc → clustergrammer_py/enrichr_functions.pyc
diff --git a/clustergrammer/export_data.py → clustergrammer_py/export_data.py b/clustergrammer/export_data.py → clustergrammer_py/export_data.py
diff --git a/clustergrammer/export_data.pyc → clustergrammer_py/export_data.pyc b/clustergrammer/export_data.pyc → clustergrammer_py/export_data.pyc
diff --git a/clustergrammer/iframe_web_app.py → clustergrammer_py/iframe_web_app.py b/clustergrammer/iframe_web_app.py → clustergrammer_py/iframe_web_app.py
diff --git a/clustergrammer/initialize_net.py → clustergrammer_py/initialize_net.py b/clustergrammer/initialize_net.py → clustergrammer_py/initialize_net.py
diff --git a/clustergrammer/initialize_net.pyc → clustergrammer_py/initialize_net.pyc b/clustergrammer/initialize_net.pyc → clustergrammer_py/initialize_net.pyc
diff --git a/clustergrammer/load_data.py → clustergrammer_py/load_data.py b/clustergrammer/load_data.py → clustergrammer_py/load_data.py
diff --git a/clustergrammer/load_data.pyc → clustergrammer_py/load_data.pyc b/clustergrammer/load_data.pyc → clustergrammer_py/load_data.pyc
diff --git a/clustergrammer/load_vect_post.py → clustergrammer_py/load_vect_post.py b/clustergrammer/load_vect_post.py → clustergrammer_py/load_vect_post.py
diff --git a/clustergrammer/make_clust_fun.py → clustergrammer_py/make_clust_fun.py b/clustergrammer/make_clust_fun.py → clustergrammer_py/make_clust_fun.py
diff --git a/clustergrammer/make_clust_fun.pyc → clustergrammer_py/make_clust_fun.pyc b/clustergrammer/make_clust_fun.pyc → clustergrammer_py/make_clust_fun.pyc
diff --git a/clustergrammer/make_sim_mat.py → clustergrammer_py/make_sim_mat.py b/clustergrammer/make_sim_mat.py → clustergrammer_py/make_sim_mat.py
diff --git a/clustergrammer/make_sim_mat.pyc → clustergrammer_py/make_sim_mat.pyc b/clustergrammer/make_sim_mat.pyc → clustergrammer_py/make_sim_mat.pyc
diff --git a/clustergrammer/make_views.py → clustergrammer_py/make_views.py b/clustergrammer/make_views.py → clustergrammer_py/make_views.py
diff --git a/clustergrammer/make_views.pyc → clustergrammer_py/make_views.pyc b/clustergrammer/make_views.pyc → clustergrammer_py/make_views.pyc
diff --git a/clustergrammer/make_viz.py → clustergrammer_py/make_viz.py b/clustergrammer/make_viz.py → clustergrammer_py/make_viz.py
diff --git a/clustergrammer/make_viz.pyc → clustergrammer_py/make_viz.pyc b/clustergrammer/make_viz.pyc → clustergrammer_py/make_viz.pyc
diff --git a/clustergrammer/normalize_fun.py → clustergrammer_py/normalize_fun.py b/clustergrammer/normalize_fun.py → clustergrammer_py/normalize_fun.py
diff --git a/clustergrammer/proc_df_labels.py → clustergrammer_py/proc_df_labels.py b/clustergrammer/proc_df_labels.py → clustergrammer_py/proc_df_labels.py
diff --git a/clustergrammer/proc_df_labels.pyc → clustergrammer_py/proc_df_labels.pyc b/clustergrammer/proc_df_labels.pyc → clustergrammer_py/proc_df_labels.pyc
diff --git a/clustergrammer/run_filter.py → clustergrammer_py/run_filter.py b/clustergrammer/run_filter.py → clustergrammer_py/run_filter.py
diff --git a/clustergrammer/run_filter.pyc → clustergrammer_py/run_filter.pyc b/clustergrammer/run_filter.pyc → clustergrammer_py/run_filter.pyc
diff --git a/docs/_build_html/.buildinfo b/docs/_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: e22f7d2efb6cf8a09998f298823ed2eb
+config: 6d951a9cf5925d085b5d376fd31212d6
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build_html/.doctrees/case_studies.doctree b/docs/_build_html/.doctrees/case_studies.doctree
diff --git a/docs/_build_html/.doctrees/clustergrammer_js.doctree b/docs/_build_html/.doctrees/clustergrammer_js.doctree
diff --git a/docs/_build_html/.doctrees/clustergrammer_py.doctree b/docs/_build_html/.doctrees/clustergrammer_py.doctree
diff --git a/docs/_build_html/.doctrees/clustergrammer_web.doctree b/docs/_build_html/.doctrees/clustergrammer_web.doctree
diff --git a/docs/_build_html/.doctrees/clustergrammer_widget.doctree b/docs/_build_html/.doctrees/clustergrammer_widget.doctree
diff --git a/docs/_build_html/.doctrees/environment.pickle b/docs/_build_html/.doctrees/environment.pickle
diff --git a/docs/_build_html/_sources/clustergrammer_py.txt b/docs/_build_html/_sources/clustergrammer_py.txt
@@ -55,7 +55,7 @@ Clustergrammer-PY generates a Network object (see `Network class definition`_),
 
 When a matrix is loaded into an instance of ``Network`` (e.g. ``net``) it is stored in the data, ``dat``, attribute. Normalization and filtering will modify the ``dat`` representation of the matrix. When the matrix is clustered (by calling :ref:`make_clust`)
 
-.. automodule:: clustergrammer
+.. automodule:: clustergrammer_py
 
 .. autoclass:: Network
     :members:

diff --git a/docs/_build_html/_sources/index.txt b/docs/_build_html/_sources/index.txt
@@ -55,7 +55,6 @@ Contents:
    building_webpage
    clustergrammer_js
    clustergrammer_py
-   clustergrammer_py_api
    app_integration
    developing_with_clustergrammer
    license

diff --git a/docs/_build_html/_static/basic.css b/docs/_build_html/_static/basic.css
@@ -85,6 +85,10 @@ div.sphinxsidebar #searchbox input[type="text"] {
     width: 170px;
 }
 
+div.sphinxsidebar #searchbox input[type="submit"] {
+    width: 30px;
+}
+
 img {
     border: 0;
     max-width: 100%;
@@ -122,8 +126,6 @@ ul.keywordmatches li.goodmatch a {
 
 table.contentstable {
     width: 90%;
-    margin-left: auto;
-    margin-right: auto;
 }
 
 table.contentstable p.biglink {
@@ -151,14 +153,9 @@ table.indextable td {
     vertical-align: top;
 }
 
-table.indextable ul {
+table.indextable dl, table.indextable dd {
     margin-top: 0;
     margin-bottom: 0;
-    list-style-type: none;
-}
-
-table.indextable > tbody > tr > td > ul {
-    padding-left: 0em;
 }
 
 table.indextable tr.pcap {
@@ -190,13 +187,6 @@ div.genindex-jumpbox {
     padding: 0.4em;
 }
 
-/* -- domain module index --------------------------------------------------- */
-
-table.modindextable td {
-    padding: 2px;
-    border-collapse: collapse;
-}
-
 /* -- general body styles --------------------------------------------------- */
 
 div.body p, div.body dd, div.body li, div.body blockquote {
@@ -231,6 +221,10 @@ div.body td {
     text-align: left;
 }
 
+.field-list ul {
+    padding-left: 1em;
+}
+
 .first {
     margin-top: 0 !important;
 }
@@ -347,6 +341,10 @@ table.docutils td, table.docutils th {
     border-bottom: 1px solid #aaa;
 }
 
+table.field-list td, table.field-list th {
+    border: 0 !important;
+}
+
 table.footnote td, table.footnote th {
     border: 0 !important;
 }
@@ -383,20 +381,6 @@ div.figure p.caption span.caption-number {
 div.figure p.caption span.caption-text {
 }
 
-/* -- field list styles ----------------------------------------------------- */
-
-table.field-list td, table.field-list th {
-    border: 0 !important;
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 /* -- other body styles ----------------------------------------------------- */
 
@@ -447,6 +431,15 @@ dl.glossary dt {
     font-size: 1.1em;
 }
 
+.field-list ul {
+    margin: 0;
+    padding-left: 1em;
+}
+
+.field-list p {
+    margin: 0;
+}
+
 .optional {
     font-size: 1.3em;
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@@ -505,13 +498,6 @@ pre {
     overflow-y: hidden;  /* fixes display issues on Chrome browsers */
 }
 
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@@ -603,16 +589,6 @@ span.eqno {
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-    z-index: 1;
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diff --git a/docs/_build_html/_static/comment-bright.png b/docs/_build_html/_static/comment-bright.png
diff --git a/docs/_build_html/_static/comment-close.png b/docs/_build_html/_static/comment-close.png
diff --git a/docs/_build_html/_static/comment.png b/docs/_build_html/_static/comment.png
diff --git a/docs/_build_html/_static/down-pressed.png b/docs/_build_html/_static/down-pressed.png
diff --git a/docs/_build_html/_static/down.png b/docs/_build_html/_static/down.png
diff --git a/docs/_build_html/_static/file.png b/docs/_build_html/_static/file.png
diff --git a/docs/_build_html/_static/jquery.js b/docs/_build_html/_static/jquery.js
diff --git a/docs/_build_html/_static/minus.png b/docs/_build_html/_static/minus.png
diff --git a/docs/_build_html/_static/plus.png b/docs/_build_html/_static/plus.png
diff --git a/docs/_build_html/_static/searchtools.js b/docs/_build_html/_static/searchtools.js
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-        end = ranges[i][1];
-        for (j = start; j <= end; j++) {
-            result[j] = true;
-        }
-    }
-    return result;
-})();
-
-function splitQuery(query) {
-    var result = [];
-    var start = -1;
-    for (var i = 0; i < query.length; i++) {
-        if (splitChars[query.charCodeAt(i)]) {
-            if (start !== -1) {
-                result.push(query.slice(start, i));
-                start = -1;
-            }
-        } else if (start === -1) {
-            start = i;
-        }
-    }
-    if (start !== -1) {
-        result.push(query.slice(start));
-    }
-    return result;
-}
-
-
-
-
 /**
  * Search Module
  */
@@ -424,7 +324,7 @@ var Search = {
     var searchterms = [];
     var excluded = [];
     var hlterms = [];
-    var tmp = splitQuery(query);
+    var tmp = query.split(/\s+/);
     var objectterms = [];
     for (i = 0; i < tmp.length; i++) {
       if (tmp[i] !== "") {
@@ -438,10 +338,6 @@ var Search = {
       }
       // stem the word
       var word = stemmer.stemWord(tmp[i].toLowerCase());
-      // prevent stemmer from cutting word smaller than two chars
-      if(word.length < 3 && tmp[i].length >= 3) {
-        word = tmp[i];
-      }
       var toAppend;
       // select the correct list
       if (word[0] == '-') {
@@ -539,8 +435,7 @@ var Search = {
             displayNextItem();
           });
         } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
-          var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
-          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
+          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
                   dataType: "text",
                   complete: function(jqxhr, textstatus) {
                     var data = jqxhr.responseText;
@@ -579,7 +474,6 @@ var Search = {
    */
   performObjectSearch : function(object, otherterms) {
     var filenames = this._index.filenames;
-    var docnames = this._index.docnames;
     var objects = this._index.objects;
     var objnames = this._index.objnames;
     var titles = this._index.titles;
@@ -633,7 +527,7 @@ var Search = {
           } else {
             score += Scorer.objPrioDefault;
           }
-          results.push([docnames[match[0]], fullname, '#'+anchor, descr, score, filenames[match[0]]]);
+          results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]);
         }
       }
     }
@@ -645,7 +539,6 @@ var Search = {
    * search for full-text terms in the index
    */
   performTermsSearch : function(searchterms, excluded, terms, titleterms) {
-    var docnames = this._index.docnames;
     var filenames = this._index.filenames;
     var titles = this._index.titles;
 
@@ -720,7 +613,7 @@ var Search = {
         // select one (max) score for the file.
         // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
         var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
-        results.push([docnames[file], titles[file], '', null, score, filenames[file]]);
+        results.push([filenames[file], titles[file], '', null, score]);
       }
     }
     return results;

diff --git a/docs/_build_html/_static/up-pressed.png b/docs/_build_html/_static/up-pressed.png
diff --git a/docs/_build_html/_static/up.png b/docs/_build_html/_static/up.png
diff --git a/docs/_build_html/app_integration.html b/docs/_build_html/app_integration.html
@@ -30,9 +30,6 @@
 
 
 
-        <link rel="index" title="Index"
-              href="genindex.html"/>
-        <link rel="search" title="Search" href="search.html"/>
     <link rel="top" title="Clustergrammer 1.0.0 documentation" href="index.html"/>
         <link rel="next" title="Developing Clustergrammer" href="developing_with_clustergrammer.html"/>
         <link rel="prev" title="Clustergrammer-PY" href="clustergrammer_py.html"/> 
@@ -138,7 +135,7 @@
       <li class="wy-breadcrumbs-aside">
 
 
-            <a href="_sources/app_integration.rst.txt" rel="nofollow"> View page source</a>
+            <a href="_sources/app_integration.txt" rel="nofollow"> View page source</a>
 
 
       </li>

diff --git a/docs/_build_html/biology_specific_features.html b/docs/_build_html/biology_specific_features.html
@@ -30,9 +30,6 @@
 
 
 
-        <link rel="index" title="Index"
-              href="genindex.html"/>
-        <link rel="search" title="Search" href="search.html"/>
     <link rel="top" title="Clustergrammer 1.0.0 documentation" href="index.html"/>
         <link rel="next" title="Case Studies" href="case_studies.html"/>
         <link rel="prev" title="Interacting with the Visualization" href="interacting_with_viz.html"/> 
@@ -136,7 +133,7 @@
       <li class="wy-breadcrumbs-aside">
 
 
-            <a href="_sources/biology_specific_features.rst.txt" rel="nofollow"> View page source</a>
+            <a href="_sources/biology_specific_features.txt" rel="nofollow"> View page source</a>
 
 
       </li>