Merge branch 'release/v1.5.2'

dputhier · Nov 6, 2021 · b20af0f · b20af0f
2 parents 815ef75 + 4c3758e
commit b20af0f
Show file tree

Hide file tree

Showing 92 changed files with 224 additions and 227 deletions.
diff --git a/README.rst b/README.rst
@@ -47,9 +47,6 @@ Documentation              |documentation|_
 .. |downloads| image:: https://anaconda.org/bioconda/pygtftk/badges/downloads.svg
 .. _downloads: https://anaconda.org/bioconda/pygtftk
 
-.. |hits| image:: http://hits.dwyl.io/dputhier/pygtftk.svg
-.. _hits: http://hits.dwyl.io/dputhier/pygtftk
-
 .. |reference| image:: https://img.shields.io/reference-yes-green.svg
 .. _reference: http://hits.dwyl.io/dputhier/pygtftk
 
@@ -143,7 +140,7 @@ Installation through setup.py
 
 This is not the preferred way for installation. Choose conda whenever possible. We have observed several issues with dependencies that still need to be fixed. ::
 
-    git clone [email protected]:dputhier/pygtftk.git pygtftk
+    git clone http://[email protected]:dputhier/pygtftk.git pygtftk
     cd pygtftk
     # Check your Python version (>=3.8,<3.9)
     pip install -r requirements.txt

diff --git a/docs/_images/example_01.png b/docs/_images/example_01.png
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/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: '1.5.1',
+    VERSION: '1.5.2',
     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_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/merge_ologram_stats_01.pdf b/docs/_static/merge_ologram_stats_01.pdf
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 1.5.1 documentation</title>
+    <title>Warning about supported GTF file formats &#8212; gtftk 1.5.2 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 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Warning about supported GTF file formats</a></li> 
       </ul>
     </div>  
@@ -201,13 +201,13 @@ <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 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 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 03, 2021.
+      Last updated on Nov 06, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>

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 1.5.1 documentation</title>
+    <title>Commands from section ‘annotation’ &#8212; gtftk 1.5.2 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 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘annotation’</a></li> 
       </ul>
     </div>  
@@ -475,13 +475,13 @@ <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 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 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 03, 2021.
+      Last updated on Nov 06, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>

diff --git a/docs/api.html b/docs/api.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Help on Python package (pygtftk) &#8212; gtftk 1.5.1 documentation</title>
+    <title>Help on Python package (pygtftk) &#8212; gtftk 1.5.2 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="miscellaneous.html" title="Commands from section ‘miscellaneous’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Help on Python package (pygtftk)</a></li> 
       </ul>
     </div>  
@@ -3737,13 +3737,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="miscellaneous.html" title="Commands from section ‘miscellaneous’"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Help on Python package (pygtftk)</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Nov 03, 2021.
+      Last updated on Nov 06, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>

diff --git a/docs/bwig_coverage.html b/docs/bwig_coverage.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>The pygtftk.bwig.bw_coverage module &#8212; gtftk 1.5.1 documentation</title>
+    <title>The pygtftk.bwig.bw_coverage module &#8212; gtftk 1.5.2 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="api.html" title="Help on Python package (pygtftk)"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">The pygtftk.bwig.bw_coverage module</a></li> 
       </ul>
     </div>  
@@ -178,13 +178,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="api.html" title="Help on Python package (pygtftk)"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">The pygtftk.bwig.bw_coverage module</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Nov 03, 2021.
+      Last updated on Nov 06, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>

diff --git a/docs/conversion.html b/docs/conversion.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘conversion’ &#8212; gtftk 1.5.1 documentation</title>
+    <title>Commands from section ‘conversion’ &#8212; gtftk 1.5.2 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="selection.html" title="Commands from section ‘selection’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘conversion’</a></li> 
       </ul>
     </div>  
@@ -320,13 +320,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="selection.html" title="Commands from section ‘selection’"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘conversion’</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Nov 03, 2021.
+      Last updated on Nov 06, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>

diff --git a/docs/coordinates.html b/docs/coordinates.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘coordinates’ &#8212; gtftk 1.5.1 documentation</title>
+    <title>Commands from section ‘coordinates’ &#8212; gtftk 1.5.2 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="ologram.html" title="Commands from section ‘ologram’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘coordinates’</a></li> 
       </ul>
     </div>  
@@ -423,13 +423,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="ologram.html" title="Commands from section ‘ologram’"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.2 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘coordinates’</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Nov 03, 2021.
+      Last updated on Nov 06, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>