Merge pull request #104 from epifluidlab/fix-delfi

Fix delfi
epifluidlab · Oct 11, 2024 · 8fb1152 · 8fb1152
2 parents ade54a1 + 5edb3b1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,14 @@ The format is based on
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.7.4] - 2024-08-24
+
+### Fixed
+ - `delfi` accepts `gap_file=None`
+ - update prog for `delfi` to reflect compatibility with reference genomes
+ other than hg19
+
 ## [0.7.4] - 2024-08-24
 
 ### Changed

diff --git a/docs/_build/doctrees/documentation/api_reference/basicfeatures.doctree b/docs/_build/doctrees/documentation/api_reference/basicfeatures.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/cleavageprofile.doctree b/docs/_build/doctrees/documentation/api_reference/cleavageprofile.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/delfi.doctree b/docs/_build/doctrees/documentation/api_reference/delfi.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/endmotifs.doctree b/docs/_build/doctrees/documentation/api_reference/endmotifs.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/fragfile.doctree b/docs/_build/doctrees/documentation/api_reference/fragfile.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/genomeutils.doctree b/docs/_build/doctrees/documentation/api_reference/genomeutils.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/index.doctree b/docs/_build/doctrees/documentation/api_reference/index.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/wps.doctree b/docs/_build/doctrees/documentation/api_reference/wps.doctree
diff --git a/docs/_build/doctrees/documentation/cli_reference/index.doctree b/docs/_build/doctrees/documentation/cli_reference/index.doctree
diff --git a/docs/_build/doctrees/documentation/index.doctree b/docs/_build/doctrees/documentation/index.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/features.doctree b/docs/_build/doctrees/documentation/user_guide/features.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/help.doctree b/docs/_build/doctrees/documentation/user_guide/help.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/index.doctree b/docs/_build/doctrees/documentation/user_guide/index.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/inputdata.doctree b/docs/_build/doctrees/documentation/user_guide/inputdata.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/installation.doctree b/docs/_build/doctrees/documentation/user_guide/installation.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/intersectpolicy.doctree b/docs/_build/doctrees/documentation/user_guide/intersectpolicy.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/quickstart.doctree b/docs/_build/doctrees/documentation/user_guide/quickstart.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/structure.doctree b/docs/_build/doctrees/documentation/user_guide/structure.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/what.doctree b/docs/_build/doctrees/documentation/user_guide/what.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
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: 670efaa449e3fccfe64f8fb2cf4a7d46
+config: 7b9a79626a3bd201c50461a4a33a6bd0
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_static/basic.css b/docs/_build/html/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -237,10 +237,6 @@ a.headerlink {
     visibility: hidden;
 }
 
-a:visited {
-    color: #551A8B;
-}
-
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -674,16 +670,6 @@ dd {
     margin-left: 30px;
 }
 
-.sig dd {
-    margin-top: 0px;
-    margin-bottom: 0px;
-}
-
-.sig dl {
-    margin-top: 0px;
-    margin-bottom: 0px;
-}
-
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -752,14 +738,6 @@ abbr, acronym {
     cursor: help;
 }
 
-.translated {
-    background-color: rgba(207, 255, 207, 0.2)
-}
-
-.untranslated {
-    background-color: rgba(255, 207, 207, 0.2)
-}
-
 /* -- code displays --------------------------------------------------------- */
 
 pre {

diff --git a/docs/_build/html/_static/doctools.js b/docs/_build/html/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js
@@ -1,4 +1,5 @@
-const DOCUMENTATION_OPTIONS = {
+var DOCUMENTATION_OPTIONS = {
+    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
     VERSION: '',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,

diff --git a/docs/_build/html/_static/language_data.js b/docs/_build/html/_static/language_data.js
@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, if available */
+/* Non-minified version is copied as a separate JS file, is available */
 
 /**
  * Porter Stemmer