Merge pull request #121 from epifluidlab/develop

Develop

CHANGELOG.md

@@ -7,6 +7,29 @@ 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
+
+### Removed
+- `strand_location` arg from `agg_bigwig`
+- `cli_hist` module
+
+### Fixed
+- fixed bug involving tqdm progress bar in `frag_length_intervals`
+- some code formatting
+- fixed bug involving arg names in `filter-bam`
+- add some missing args to CLI
+
+### 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
+
+### Added
+- internal `utils._typing` and `utils._deprecation` modules
+- test for `delfi`
+
 ## [0.8.0] - 2024-12-04
 
 ### Removed
@@ -27,12 +50,14 @@ that is more memory efficient.
 - `finaletoolkit.frag.frag_length_bins` and
 `finaletoolkit.frag.frag_length_intervals` now take `min_length` and 
 `max_length` keyword args to only consider fragments of certain lengths.
-- flags for `frag-length-bins` and `frag-length-intervals` CLI commands updated to match Python API
+- flags for `frag-length-bins` and `frag-length-intervals` CLI commands updated
+to match Python API
 - `coverage` default argument for `normalize` changed to `False` 
 - `coverage` default argument for `scale_factor` changed to 1. 
 
 ### Added
 - `finaletoolkit.frag.frag_length_bins` can generate a histogram figure
+- tests for `frag_length` module
 
 ## [0.7.8] - 2024-11-28
 
@@ -41,10 +66,11 @@ that is more memory efficient.
 `site_bed` must be sorted.
 
 ### Added
-- `normalize` keyword argument and `--normalize` flag to `finaletoolkit.frag.coverage` function and `finaletoolkit coverage` subcommand, respectively. Setting this argument/flag to true results in the output
+- `normalize` keyword argument and `--normalize` flag to
+`finaletoolkit.frag.coverage` function and `finaletoolkit coverage` subcommand,
+respectively. Setting this argument/flag to true results in the output
 being normalized by the total coverage, ignoring `scale_factor` if specified.
-- `--intersect-policy` or `-p` flag added to `finaletoolkit coverage` subcommand.
-- tests for `frag_length` module
+- `--intersect-policy` or `-p` flag added to `finaletoolkit coverage`subcommand.
 
 ## [0.7.7] - 2024-11-27
 
@@ -93,15 +119,18 @@ information when calculating end motifs on forward-strand only.
  - Added a test for the coverage function
 
 ### Fixed
- - Ensured that the coverage value returns the expected value (previously returned an empty generator)
+ - Ensured that the coverage value returns the expected value (previously
+ returned an empty generator)
 
 ## [0.7.2] - 2024-08-17
 
 ### Changed
- - Included `output_file` as required argument for `finaletoolkit cleavage-profile`.
+ - Included `output_file` as required argument for
+ `finaletoolkit cleavage-profile`.
 
 ### Fixed
- - Fixed incompatible types in min function through an explicit cast of chrom_sizes to integers.
+ - Fixed incompatible types in min function through an explicit cast of
+ chrom_sizes to integers.
 
 ## [0.7.1] - 2024-08-11
 
@@ -219,11 +248,13 @@ are specified without `contig`
 ## [0.5.2] - 2024-05-08
 
 ### Fixed
-- `interval-mds` CLI subcommand calculates correctly without large negative values.
+- `interval-mds` CLI subcommand calculates correctly without large negative
+values.
 - `interval-mds` CLI subcommand now correctly parses tsv files.
 
 ### Added
-- Most end-motif related Python functions accept Path instances as inputs for files.
+- Most end-motif related Python functions accept Path instances as inputs for
+files.
 - Unit and function tests, especially for end-motif related functions.
 
 
@@ -235,7 +266,8 @@ are specified without `contig`
 - Update contacts in TOML
 
 ### Fixed
-- `interval-mds` and `mds` both calculate correctly when one motif has a frequency of 0
+- `interval-mds` and `mds` both calculate correctly when one motif has a
+frequency of 0
 
 ## [0.5.0] - 2024-04-24
 

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

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 {

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.
  *
  */

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,

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

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.
+ */