Merge branch 'release/v1.5.0'

dputhier · Nov 3, 2021 · aaf3abe · aaf3abe
2 parents 7173d2c + 65c48d2
commit aaf3abe
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diff --git a/README.rst b/README.rst
@@ -101,6 +101,12 @@ Documentation about OLOGRAM (OverLap Of Genomic Regions Analysis using Monte Car
 
 **NB:** The readthedoc version won't be maintained and will be closed in the near future. This choice was motivated by the impossibility to maintain a dynamic documentation (using sphinx/sphinxcontrib-programoutput) given the computing time provided by readthedoc server.
 
+Note that example dataset are available to test the various subcommands (see `documentation page <https://dputhier.github.io/pygtftk/information.html#get-example>`_).
+
+    gtftk get_example  -h
+    # E.g. to get all file from the 'simple' dataset
+    gtftk get_example -d simple -f "*"
+
 
 System requirements
 --------------------
@@ -112,14 +118,13 @@ At the moment, the gtftk program has been tested on:
   - Linux (Ubuntu 12.04 and 18.04)
   - OSX (Yosemite, El Capitan, Mojave).
 
-
 Installation
 -------------
 
 Installation through conda package building
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Installation through **conda** should be the **preferred install solution**. The pygtftk package and gtftk command line tool require external dependencies with some version constrains.
+Installation through **conda** should be the **preferred install solution**. The pygtftk package and gtftk command line tool require external dependencies (bedtools ">v2.23.1", graphviz, unzip) with some version constrains.
 
 If conda is not available on your system, first install miniconda from the official `web site <http://conda.pydata.org/miniconda.html>`_ and make sure you have bioconda and conda-forge channels set up in the order below. ::
 
@@ -140,7 +145,7 @@ This is not the preferred way for installation. Choose conda whenever possible.
 
     git clone [email protected]:dputhier/pygtftk.git pygtftk
     cd pygtftk
-    # Check your Python version (>=3.5,<3.7)
+    # Check your Python version (>=3.8,<3.9)
     pip install -r requirements.txt
     python setup.py install
 

diff --git a/changelog.md b/changelog.md
@@ -2,6 +2,27 @@
 # Changelog
 
 
+## v1.5.0
+
+### Bug Fixes
+
+* 
+
+### API/CLI Changes
+
+
+### Code changes
+
+* OLOGRAM README has been  updated (add bedtools, graphviz and unzip dependency).
+
+* Replace operatorPrecedence with infixNotation when using pyparsing (see #166).
+
+### New Features
+
+
+# Changelog
+
+
 ## v1.4.0
 
 ### Bug Fixes

diff --git a/docs/_images/example_01.png b/docs/_images/example_01.png
diff --git a/docs/_images/example_01b.png b/docs/_images/example_01b.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: '1.4.0',
+    VERSION: '1.5.0',
     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_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 1.4.0 documentation</title>
+    <title>Warning about supported GTF file formats &#8212; gtftk 1.5.0 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 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 Aug 31, 2021.
+      Last updated on Nov 03, 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 1.4.0 documentation</title>
+    <title>Commands from section ‘annotation’ &#8212; gtftk 1.5.0 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 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 Aug 31, 2021.
+      Last updated on Nov 03, 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 1.4.0 documentation</title>
+    <title>Help on Python package (pygtftk) &#8212; gtftk 1.5.0 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="miscellaneous.html" title="Commands from section ‘miscellaneous’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 Aug 31, 2021.
+      Last updated on Nov 03, 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 1.4.0 documentation</title>
+    <title>The pygtftk.bwig.bw_coverage module &#8212; gtftk 1.5.0 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="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 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 Aug 31, 2021.
+      Last updated on Nov 03, 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 1.4.0 documentation</title>
+    <title>Commands from section ‘conversion’ &#8212; gtftk 1.5.0 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="selection.html" title="Commands from section ‘selection’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 Aug 31, 2021.
+      Last updated on Nov 03, 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 1.4.0 documentation</title>
+    <title>Commands from section ‘coordinates’ &#8212; gtftk 1.5.0 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="ologram.html" title="Commands from section ‘ologram’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 1.4.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.5.0 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 Aug 31, 2021.
+      Last updated on Nov 03, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>