Merge remote-tracking branch 'origin/development'

# Conflicts:
#	.github/workflows/build_ci.yml
#	HISTORY.rst
#	README.rst
#	docs/build/.doctrees/api_reference.doctree
#	docs/build/.doctrees/environment.pickle
#	docs/build/.doctrees/history.doctree
#	docs/build/.doctrees/readme.doctree
#	docs/build/.doctrees/rnalysis.doctree
#	docs/build/.doctrees/tutorial.doctree
#	docs/build/history.html
#	docs/build/readme.html
#	docs/build/rnalysis.filtering.CountFilter.save_csv.html
#	docs/build/rnalysis.filtering.CountFilter.scatter_sample_vs_sample.html
#	docs/build/rnalysis.filtering.DESeqFilter.save_csv.html
#	docs/build/rnalysis.filtering.DESeqFilter.sort.html
#	docs/build/rnalysis.filtering.Filter.save_csv.html
#	docs/build/rnalysis.filtering.Filter.sort.html
#	docs/build/rnalysis.filtering.FoldChangeFilter.save_csv.html
#	docs/build/rnalysis.filtering.FoldChangeFilter.sort.html
#	docs/build/searchindex.js
#	rnalysis/enrichment.py

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.8.0
+current_version = 3.9.0
 commit = True
 tag = False
 

.github/workflows/build_ci.yml

@@ -139,6 +139,7 @@ jobs:
             -   name: Coveralls Parallel
                 uses: coverallsapp/github-action@v2
                 if: runner.os != 'macOS'
+                continue-on-error: true
                 with:
                     flag-name: run-${{ join(matrix.*, '-') }}
                     parallel: true
@@ -152,5 +153,6 @@ jobs:
         steps:
             -   name: Coveralls Finished
                 uses: coverallsapp/github-action@v2
+                continue-on-error: true
                 with:
                     parallel-finished: true

.github/workflows/pyinstaller.yml

@@ -62,17 +62,17 @@ jobs:
                         CMD_BUILD: >
                             pyinstaller RNAlysis.spec &&
                             cd dist/ &&
-                            zip -r RNAlysis-3.8.0_macos.zip ./RNAlysis* &&
+                            zip -r RNAlysis-3.9.0_macos.zip ./RNAlysis* &&
                             ls -ltr
-                        OUT_FILE_NAME: RNAlysis-3.8.0_macos.zip
+                        OUT_FILE_NAME: RNAlysis-3.9.0_macos.zip
                         ASSET_MIME: application/zip
                     -   os: windows-latest
                         TARGET: windows
                         CMD_BUILD: >
                             pyinstaller RNAlysis.spec &&
                             cd dist/ &&
-                            7z a RNAlysis-3.8.0_windows.zip -r "RNAlysis-3.8.0/"
-                        OUT_FILE_NAME: RNAlysis-3.8.0_windows.zip
+                            7z a RNAlysis-3.9.0_windows.zip -r "RNAlysis-3.9.0/"
+                        OUT_FILE_NAME: RNAlysis-3.9.0_windows.zip
                         ASSET_MIME: application/zip
         steps:
             -   name: Checkout repository

HISTORY.rst

@@ -2,13 +2,50 @@
 History
 =======
 
-3.8.1 (2023-05-??)
+3.9.0 (2023-06-09)
 ------------------
+Version 3.9.0 of RNALysis introduces several enhancements and fixes to improve your experience.
+The release includes additional enrichment plot styles, a new option for PCA plots,
+the ability to load and save data tables in Parquet format, and new actions in the Help menu for reporting issues and suggesting improvements.
+The update also improves the performance of various functions, ensures consistency in font and theme settings,
+and addresses multiple bug fixes, including issues with automatic session reports and visualization functions.
+
+Added
+*******
+* Added additional parameters to enrichment bar plots (enrichment.enrichment_bar_plot), including a new plot style ('lollipop') and observed/expected labels on the graph.
+* Added a new parameter to Principal Component Analysis plots (CountFilter.pca) 'plot_grid', which can enable or disable adding a grid to PCA plots.
+* RNAlysis can now load and save data tables in Parquet format (.parquet)
+* Added new actions to the Help menu, allowing users to report issues, suggest issues, or open discussions.
+
+Changed
+********
+* Functions in the FASTQ model are now added to automatic session reports.
+* Many of the functions in RNAlysis should now run faster.
+* Font type, size, and color for help tooltips should now match the global font settings.
+* True/False toggle switches now scale with font size.
+* When loading data tables into RNAlysis, you will now see only supported file formats by default.
+* Clustering PCA plots are now plotted in proportion to the % variance explained by each PC.
+* The legend in clustering PCA plots is now draggable.
 
 Fixed
 *******
+* Fixed bug where data tables generated through the FASTQ model would not display properly in automatic session reports.
 * Fixed bug where graphs generated through the Visualize Gene Sets window would not be added to automatic analysis report.
 * When saving a file through the graphical interface, automatically-suggested filenames no longer contain illegal characters.
+* Improved clarity of error message when R installation folder is not found.
+* Fixed bug where some input parameter widgets in the RNAlysis graphical interface would not display properly.
+* RNAlysis now provides a clearer warning message when attempting to run HDBSCAN clustering, if the hdbscan package is not installed.
+* Label text in PCA plots and hierarchical clustergrams should no longer be cropped outside of the visible region of the plot.
+* Fixed bug where some visualization functions, such as pair-plot (CountFilter.pairplot) would not display properly due to version mismatches between pandas and seaborn.
+* Improved clarity of error messages when external apps' (kallisto, bowtie2, etc) installation folders are not found.
+* Fixed bug where running the RNAlysis graphical interface on a new computer would sometimes raise an error (thanks to `NeuroRookie <https://github.com/NeuroRookie>`_ in `#25 <https://github.com/GuyTeichman/RNAlysis/issues/25>`_).
+* Fixed a bug where the 'min_samples' parameter in HDBSCAN clustering could not be disabled.
+* Fixed a bug where applying a function to a gene set with inplace=False would cause the new gene set to be called 'New Table'.
+* Fixed a bug where RNAlysis would display the message "Pipeline saved successfully", even when the user cancels the save operation.
+
+New Contributors
+*****************
+* `NeuroRookie`_ in `#25`_
 
 3.8.0 (2023-05-07)
 ------------------

README.rst

@@ -188,6 +188,7 @@ Contributors
 * Matthias Wilm
 * `sandyl27 <https://github.com/sandyl27>`_
 * `clockgene <https://github.com/clockgene>`_
+* `NeuroRookie <https://github.com/NeuroRookie>`_
 
 ----
 

RNAlysis.spec

@@ -89,5 +89,5 @@ if not is_darwin:
         strip=False,
         upx=True,
         upx_exclude=[],
-        name='RNAlysis-3.8.0',
+        name='RNAlysis-3.9.0',
     )

docs/build/.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: 3c48e481a1029f13bde63990a1e048d4
+config: 2858b2fb37c09d1c89cf9b770d3cf048
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/_sources/rnalysis.filtering.CountFilter.rst.txt

@@ -62,6 +62,8 @@ rnalysis.filtering.CountFilter
     CountFilter.plot_expression
     CountFilter.print_features
     CountFilter.save_csv
+    CountFilter.save_parquet
+    CountFilter.save_table
     CountFilter.scatter_sample_vs_sample
     CountFilter.sort
     CountFilter.split_by_attribute

docs/build/_sources/rnalysis.filtering.CountFilter.save_parquet.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.save\_parquet
+============================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.save_parquet

docs/build/_sources/rnalysis.filtering.CountFilter.save_table.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.save\_table
+==========================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.save_table

docs/build/_sources/rnalysis.filtering.DESeqFilter.rst.txt

@@ -41,6 +41,8 @@ rnalysis.filtering.DESeqFilter
     DESeqFilter.number_filters
     DESeqFilter.print_features
     DESeqFilter.save_csv
+    DESeqFilter.save_parquet
+    DESeqFilter.save_table
     DESeqFilter.sort
     DESeqFilter.split_by_attribute
     DESeqFilter.split_by_percentile

docs/build/_sources/rnalysis.filtering.DESeqFilter.save_parquet.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.DESeqFilter.save\_parquet
+============================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: DESeqFilter.save_parquet

docs/build/_sources/rnalysis.filtering.DESeqFilter.save_table.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.DESeqFilter.save\_table
+==========================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: DESeqFilter.save_table

docs/build/_sources/rnalysis.filtering.Filter.rst.txt

@@ -38,6 +38,8 @@ rnalysis.filtering.Filter
     Filter.number_filters
     Filter.print_features
     Filter.save_csv
+    Filter.save_parquet
+    Filter.save_table
     Filter.sort
     Filter.split_by_attribute
     Filter.split_by_percentile

docs/build/_sources/rnalysis.filtering.Filter.save_parquet.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.Filter.save\_parquet
+=======================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: Filter.save_parquet

docs/build/_sources/rnalysis.filtering.Filter.save_table.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.Filter.save\_table
+=====================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: Filter.save_table

docs/build/_sources/rnalysis.filtering.FoldChangeFilter.rst.txt

@@ -41,6 +41,8 @@ rnalysis.filtering.FoldChangeFilter
     FoldChangeFilter.print_features
     FoldChangeFilter.randomization_test
     FoldChangeFilter.save_csv
+    FoldChangeFilter.save_parquet
+    FoldChangeFilter.save_table
     FoldChangeFilter.sort
     FoldChangeFilter.split_by_attribute
     FoldChangeFilter.split_by_percentile

docs/build/_sources/rnalysis.filtering.FoldChangeFilter.save_parquet.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.FoldChangeFilter.save\_parquet
+=================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: FoldChangeFilter.save_parquet

docs/build/_sources/rnalysis.filtering.FoldChangeFilter.save_table.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.FoldChangeFilter.save\_table
+===============================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: FoldChangeFilter.save_table

docs/build/_sources/tutorial.rst.txt

@@ -445,7 +445,7 @@ Let's set the statistical test to 'hypergeometric', the organism to 'Caenorhabdi
 
 We will leave the rest of the settings on the default values, but keep in mind that you can customize the analysis to a significant degree: using different statistical tests (including a statistical test that doesn't require a background gene set), using only specific types of GO annotations, propagating the annotations differently, etc'. You can read more about these options in the complete user guide.
 
-Scroll to the bottom of thw window and click on the "run" button to run the analysis:
+Scroll to the bottom of the window and click on the "run" button to run the analysis:
 
 .. image:: /tutorial_screenshots/01h04_go_enrichment.png
   :width: 600
@@ -1144,7 +1144,7 @@ Let's set the statistical test to 'randomization', and then set the name of our
   :width: 600
   :alt: Enrichment analysis - set the attributes to enrich for
 
-Scroll to the bottom of thw window and click on the "run" button to run the analysis:
+Scroll to the bottom of the window and click on the "run" button to run the analysis:
 
 .. image:: /tutorial_screenshots/02h06_enrichment.png
   :width: 600

docs/build/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '3.8.0',
+    VERSION: '3.9.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',