Merge branch 'release/v1.6.0'

dputhier · Feb 25, 2022 · a418967 · a418967
2 parents 8ffa3d6 + b38e45b
commit a418967
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diff --git a/.gitignore b/.gitignore
@@ -84,6 +84,9 @@ target/
 # VSCode
 .vscode
 
+# PyCharm
+.idea
+
 # pyenv
 .python-version
 

diff --git a/Makefile b/Makefile
@@ -237,10 +237,10 @@ release_pip_osx:
 	@ echo "# Creating osx compliant package (pip)          #"
 	@ echo "#-----------------------------------------------#"
 	@ mkdir -p wheels
-	@ conda create -n  python_dev_38 python=3.8 -y; \
-	conda activate python_dev_38                          ; \
+	@ conda create -n  python_dev_39 python=3.9 -y; \
+	conda activate python_dev_39                          ; \
 	pip install -r requirements.txt ; \
-	rm -rf dist build; python3.8 setup.py bdist_wheel             ; \
+	rm -rf dist build; python3.9 setup.py bdist_wheel             ; \
 	cp dist/*whl wheels                                          ; \
 	rm -rf dist build
 

diff --git a/docs/_images/example_02.png b/docs/_images/example_02.png
diff --git a/docs/_images/example_05.png b/docs/_images/example_05.png
diff --git a/docs/_images/example_06.png b/docs/_images/example_06.png
diff --git a/docs/_images/example_06b.png b/docs/_images/example_06b.png
diff --git a/docs/_images/example_07.png b/docs/_images/example_07.png
diff --git a/docs/_images/example_08.png b/docs/_images/example_08.png
diff --git a/docs/_images/example_13.png b/docs/_images/example_13.png
diff --git a/docs/_static/basic.css b/docs/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -731,8 +731,9 @@ dl.glossary dt {
 
 .classifier:before {
     font-style: normal;
-    margin: 0.5em;
+    margin: 0 0.5em;
     content: ":";
+    display: inline-block;
 }
 
 abbr, acronym {
@@ -756,6 +757,7 @@ span.pre {
     -ms-hyphens: none;
     -webkit-hyphens: none;
     hyphens: none;
+    white-space: nowrap;
 }
 
 div[class*="highlight-"] {
@@ -819,7 +821,7 @@ div.code-block-caption code {
 
 table.highlighttable td.linenos,
 span.linenos,
-div.doctest > div.highlight span.gp {  /* gp: Generic.Prompt */
+div.highlight span.gp {  /* gp: Generic.Prompt */
   user-select: none;
   -webkit-user-select: text; /* Safari fallback only */
   -webkit-user-select: none; /* Chrome/Safari */

diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -264,6 +264,9 @@ var Documentation = {
   hideSearchWords : function() {
     $('#searchbox .highlight-link').fadeOut(300);
     $('span.highlighted').removeClass('highlighted');
+    var url = new URL(window.location);
+    url.searchParams.delete('highlight');
+    window.history.replaceState({}, '', url);
   },
 
   /**
@@ -301,12 +304,14 @@ var Documentation = {
               window.location.href = prevHref;
               return false;
             }
+            break;
           case 39: // right
             var nextHref = $('link[rel="next"]').prop('href');
             if (nextHref) {
               window.location.href = nextHref;
               return false;
             }
+            break;
         }
       }
     });

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.5.3',
+    VERSION: '1.6.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/_static/example_01.png b/docs/_static/example_01.png
diff --git a/docs/_static/example_01b.png b/docs/_static/example_01b.png
diff --git a/docs/_static/example_02.png b/docs/_static/example_02.png
diff --git a/docs/_static/example_05.png b/docs/_static/example_05.png
diff --git a/docs/_static/example_06.png b/docs/_static/example_06.png
diff --git a/docs/_static/example_06b.png b/docs/_static/example_06b.png
diff --git a/docs/_static/example_07.png b/docs/_static/example_07.png
diff --git a/docs/_static/example_08.png b/docs/_static/example_08.png
diff --git a/docs/_static/example_13.png b/docs/_static/example_13.png
diff --git a/docs/_static/example_pa_01.pdf b/docs/_static/example_pa_01.pdf
diff --git a/docs/_static/example_pa_02.pdf b/docs/_static/example_pa_02.pdf
diff --git a/docs/_static/example_pa_03.pdf b/docs/_static/example_pa_03.pdf
diff --git a/docs/_static/example_pa_04.pdf b/docs/_static/example_pa_04.pdf
diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js
@@ -5,7 +5,7 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/docs/_static/merge_ologram_stats_01.pdf b/docs/_static/merge_ologram_stats_01.pdf
diff --git a/docs/_static/nature.css b/docs/_static/nature.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- nature theme.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -282,7 +282,10 @@ var Search = {
                   complete: function(jqxhr, textstatus) {
                     var data = jqxhr.responseText;
                     if (data !== '' && data !== undefined) {
-                      listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
+                      var summary = Search.makeSearchSummary(data, searchterms, hlterms);
+                      if (summary) {
+                        listItem.append(summary);
+                      }
                     }
                     Search.output.append(listItem);
                     setTimeout(function() {
@@ -325,7 +328,9 @@ var Search = {
     var results = [];
 
     for (var prefix in objects) {
-      for (var name in objects[prefix]) {
+      for (var iMatch = 0; iMatch != objects[prefix].length; ++iMatch) {
+        var match = objects[prefix][iMatch];
+        var name = match[4];
         var fullname = (prefix ? prefix + '.' : '') + name;
         var fullnameLower = fullname.toLowerCase()
         if (fullnameLower.indexOf(object) > -1) {
@@ -339,7 +344,6 @@ var Search = {
           } else if (parts[parts.length - 1].indexOf(object) > -1) {
             score += Scorer.objPartialMatch;
           }
-          var match = objects[prefix][name];
           var objname = objnames[match[1]][2];
           var title = titles[match[0]];
           // If more than one term searched for, we require other words to be
@@ -498,6 +502,9 @@ var Search = {
    */
   makeSearchSummary : function(htmlText, keywords, hlwords) {
     var text = Search.htmlToText(htmlText);
+    if (text == "") {
+      return null;
+    }
     var textLower = text.toLowerCase();
     var start = 0;
     $.each(keywords, function() {

diff --git a/docs/_static/treeified.pdf b/docs/_static/treeified.pdf
diff --git a/docs/about.html b/docs/about.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Warning about supported GTF file formats &#8212; gtftk 1.5.3 documentation</title>
+    <title>Warning about supported GTF file formats &#8212; gtftk 1.6.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/nature.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="Welcome to pygtftk documentation page"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.6.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Warning about supported GTF file formats</a></li> 
       </ul>
     </div>  
@@ -151,20 +151,26 @@ <h2>Naming conventions<a class="headerlink" href="#naming-conventions" title="Pe
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
-  <h3><a href="index.html">Table of Contents</a></h3>
-  <ul>
+  <div>
+    <h3><a href="index.html">Table of Contents</a></h3>
+    <ul>
 <li><a class="reference internal" href="#">Warning about supported GTF file formats</a><ul>
 <li><a class="reference internal" href="#naming-conventions">Naming conventions</a></li>
 </ul>
 </li>
 </ul>
 
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="index.html"
-                        title="previous chapter">Welcome to pygtftk documentation page</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="installation.html"
-                        title="next chapter">Installing pygtftk/gtftk</a></p>
+  </div>
+  <div>
+    <h4>Previous topic</h4>
+    <p class="topless"><a href="index.html"
+                          title="previous chapter">Welcome to pygtftk documentation page</a></p>
+  </div>
+  <div>
+    <h4>Next topic</h4>
+    <p class="topless"><a href="installation.html"
+                          title="next chapter">Installing pygtftk/gtftk</a></p>
+  </div>
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
     <ul class="this-page-menu">
@@ -176,7 +182,7 @@ <h3>This Page</h3>
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>
@@ -201,14 +207,14 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="Welcome to pygtftk documentation page"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.6.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Warning about supported GTF file formats</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Nov 06, 2021.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
+      Last updated on Feb 25, 2022.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.4.0.
     </div>
   </body>
 </html>
diff --git a/docs/annotation.html b/docs/annotation.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘annotation’ &#8212; gtftk 1.5.3 documentation</title>
+    <title>Commands from section ‘annotation’ &#8212; gtftk 1.6.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/nature.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="conversion.html" title="Commands from section ‘conversion’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.6.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘annotation’</a></li> 
       </ul>
     </div>  
@@ -420,8 +420,9 @@ <h2>intron_sizes<a class="headerlink" href="#intron-sizes" title="Permalink to t
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
-  <h3><a href="index.html">Table of Contents</a></h3>
-  <ul>
+  <div>
+    <h3><a href="index.html">Table of Contents</a></h3>
+    <ul>
 <li><a class="reference internal" href="#">Commands from section ‘annotation’</a><ul>
 <li><a class="reference internal" href="#closest-genes">closest_genes</a></li>
 <li><a class="reference internal" href="#overlapping">overlapping</a></li>
@@ -433,12 +434,17 @@ <h3><a href="index.html">Table of Contents</a></h3>
 </li>
 </ul>
 
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="conversion.html"
-                        title="previous chapter">Commands from section ‘conversion’</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="ologram.html"
-                        title="next chapter">Commands from section ‘ologram’</a></p>
+  </div>
+  <div>
+    <h4>Previous topic</h4>
+    <p class="topless"><a href="conversion.html"
+                          title="previous chapter">Commands from section ‘conversion’</a></p>
+  </div>
+  <div>
+    <h4>Next topic</h4>
+    <p class="topless"><a href="ologram.html"
+                          title="next chapter">Commands from section ‘ologram’</a></p>
+  </div>
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
     <ul class="this-page-menu">
@@ -450,7 +456,7 @@ <h3>This Page</h3>
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>
@@ -475,14 +481,14 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="conversion.html" title="Commands from section ‘conversion’"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.6.0 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘annotation’</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Nov 06, 2021.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
+      Last updated on Feb 25, 2022.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.4.0.
     </div>
   </body>
 </html>