Merge pull request #122 from epifluidlab/develop

Develop

CHANGELOG.md

@@ -7,7 +7,7 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.9.0] - 2024-12-10
+## [0.9.0] - 2024-12-13
 
 ### Removed
 - `strand_location` arg from `agg_bigwig`
@@ -18,18 +18,30 @@ and this project adheres to
 - some code formatting
 - fixed bug involving arg names in `filter-bam`
 - add some missing args to CLI
+- issues with running `cleavage-profile` (#115)
+- issues with writing to bigwig with `wps`
 
 ### Changed
 - change default of arg `both_strands` of `end_motifs` to True to match
 behavior of original scripts
 - rename `fraction_high` and `fraction_low` to  `min_length` and `max_length`
 for all features, deprecating old args as aliases if needed.
 - numpy 2 compatible
+- fragmentomics functions assume Tabix indexed files all follow the
+FinaleDB Frag.gz file format. That is, columns are `chrom`, `start`, `stop`,
+`score`, and `strand`. If more columns are detect, a warning is issued, and
+FinaleToolkit will attempt to parse the file as a BED6 format.
+- renamed `genome_file` to `chrom_sizes` for most functions.
+- `multi_wps` and `multi_cleavage_profile` no longer return a value due to memory issues when attempting to calculate these genomewide. Instead, users should refer to the file specified with `output_file`.
 
 ### Added
 - internal `utils._typing` and `utils._deprecation` modules
 - test for `delfi`
 
+### Deprecated
+- `delfi-gc-correct` command. GC-correction is performed automatically by `delfi`
+already.
+
 ## [0.8.0] - 2024-12-04
 
 ### Removed

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

docs/_build/html/_sources/documentation/user_guide/quickstart.rst.txt

@@ -34,3 +34,5 @@ If you want to load a *specific* function, you can do so by using the following:
 Assuming we wanted to load the DELFI function::
 
     >>> from finaletoolkit.frag import delfi
+
+For more detailed tutorials, please check out our [wiki](https://github.com/epifluidlab/FinaleToolkit/wiki).

docs/_build/html/_sources/index.rst.txt

@@ -11,6 +11,7 @@ FinaleToolkit (FragmentatIoN AnaLysis of cEll-free DNA Toolkit) is a package and
 - **Website:** https://epifluidlab.github.io/finaletoolkit-docs/
 - **PyPI:** https://pypi.org/project/finaletoolkit/
 - **Documentation:** https://epifluidlab.github.io/finaletoolkit-docs/documentation
+- **Wiki:** https://github.com/epifluidlab/FinaleToolkit/wiki
 - **Source code:** https://github.com/epifluidlab/finaletoolkit
 - **Changelog:** https://github.com/epifluidlab/FinaleToolkit/blob/main/CHANGELOG.md
 - **Bug reports:** https://github.com/epifluidlab/finaletoolkit/issues

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 {

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.
  *
  */

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,

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