Merge pull request #127 from epifluidlab/develop

0.10.0
epifluidlab · Dec 19, 2024 · 942a3bd · 942a3bd
2 parents 4388de0 + 45fadbc
commit 942a3bd
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,26 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.10.0] - 2024-12-18
+
+### Changed
+- several modules containing implementations of fragmentomic features or
+utiliy functions have been made internal. This means there is now only one
+obvious import for each function. For example, `multi_wps` is imported from
+`finaletoolkit.frag`, and no longer can be imported from
+`finaletoolkit.frag.multi_wps`
+- The CLI now uses lazy importing, drastically speeding up finaletoolkit when
+called from a command line.
+- Added `negative_strand` option for end motifs related functions. When
+used in conjunction with `both_strands`, only end motifs on the negative
+(Crick) strand are considered in calculations.
+- Renamed `fraction_high` and `fraction_low` in `utils.utils.frag_generator`
+to `min_length` and `max_length`.
+
+### Fixed
+- deprecated arguments for `end-motifs` had default values which could
+lead to an error. This is fixed.
+
 ## [0.9.1] - 2024-12-17
 
 ### Fixed

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: 7b9a79626a3bd201c50461a4a33a6bd0
+config: 670efaa449e3fccfe64f8fb2cf4a7d46
 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 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ 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;
@@ -738,6 +752,14 @@ 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 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 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
@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     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 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 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, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer

diff --git a/docs/_build/html/_static/scripts/bootstrap.js.map b/docs/_build/html/_static/scripts/bootstrap.js.map
diff --git a/docs/_build/html/_static/scripts/fontawesome.js b/docs/_build/html/_static/scripts/fontawesome.js
diff --git a/docs/_build/html/_static/scripts/fontawesome.js.LICENSE.txt b/docs/_build/html/_static/scripts/fontawesome.js.LICENSE.txt
@@ -0,0 +1,5 @@
+/*!
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2024 Fonticons, Inc.
+ */
diff --git a/docs/_build/html/_static/scripts/fontawesome.js.map b/docs/_build/html/_static/scripts/fontawesome.js.map
diff --git a/docs/_build/html/_static/scripts/pydata-sphinx-theme.js b/docs/_build/html/_static/scripts/pydata-sphinx-theme.js
diff --git a/docs/_build/html/_static/scripts/pydata-sphinx-theme.js.map b/docs/_build/html/_static/scripts/pydata-sphinx-theme.js.map