Merge remote-tracking branch 'origin/development'

# Conflicts:
#	requirements.txt

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.9.2
+current_version = 3.10.0
 commit = True
 tag = False
 

.github/workflows/build_ci.yml

@@ -21,6 +21,14 @@ jobs:
         env:
             DISPLAY: ':99.0'
         steps:
+            -   name: Configure pagefile
+                if: runner.os == 'Windows'
+                uses: al-cheb/[email protected]
+
+            -   name: Set up pagefile
+                if: runner.os == 'Windows'
+                run: |
+                    (Get-CimInstance Win32_PageFileUsage).AllocatedBaseSize
             -   name: Get repository
                 uses: actions/checkout@v3
             -   name: apt-get update (Linux)
@@ -50,7 +58,7 @@ jobs:
             -   name: Install R
                 uses: r-lib/actions/setup-r@v2
                 with:
-                    r-version: '4.2.3' # The R version to download (if necessary) and use.
+                    r-version: '4.3' # The R version to download (if necessary) and use.
             -   name: Install homebrew on Linux
                 if: runner.os == 'Linux'
                 uses: Homebrew/actions/setup-homebrew@master
@@ -77,7 +85,7 @@ jobs:
                          brew install kallisto
                     elif [ "$RUNNER_OS" == "Windows" ]; then
                          choco install wget -y
-                         wget  https://github.com/pachterlab/kallisto/releases/download/v0.48.0/kallisto_windows-v0.48.0.zip
+                         wget  https://github.com/pachterlab/kallisto/releases/download/v0.50.0/kallisto_windows-v0.50.0.zip
                          7z x kallisto*.zip
                          echo "${GITHUB_WORKSPACE}/kallisto" >> $GITHUB_PATH
                     else

.github/workflows/pyinstaller.yml

@@ -62,17 +62,17 @@ jobs:
                         CMD_BUILD: >
                             pyinstaller RNAlysis.spec &&
                             cd dist/ &&
-                            zip -r RNAlysis-3.9.2_macos.zip ./RNAlysis* &&
+                            zip -r RNAlysis-3.10.0_macos.zip ./RNAlysis* &&
                             ls -ltr
-                        OUT_FILE_NAME: RNAlysis-3.9.2_macos.zip
+                        OUT_FILE_NAME: RNAlysis-3.10.0_macos.zip
                         ASSET_MIME: application/zip
                     -   os: windows-latest
                         TARGET: windows
                         CMD_BUILD: >
                             pyinstaller RNAlysis.spec &&
                             cd dist/ &&
-                            7z a RNAlysis-3.9.2_windows.zip -r "RNAlysis-3.9.2/"
-                        OUT_FILE_NAME: RNAlysis-3.9.2_windows.zip
+                            7z a RNAlysis-3.10.0_windows.zip -r "RNAlysis-3.10.0/"
+                        OUT_FILE_NAME: RNAlysis-3.10.0_windows.zip
                         ASSET_MIME: application/zip
         steps:
             -   name: Checkout repository

HISTORY.rst

@@ -2,6 +2,46 @@
 History
 =======
 
+
+3.10.0 (2023-10-31)
+------------------
+
+I'm thrilled to introduce RNAlysis version 3.10.0.
+This version includes features that were requested by users for a while, alongside quality-of-life improvements and bug fixes.
+Here is a brief highlight of the most important additions:
+
+**Ortholog Mapping:** *RNAlysis* can now map genes to their closest orthologs in different organisms.
+You can map genes to their orthologs using four different databases - Ensembl, Panther, PhylomeDB, and OrthoInspector - extracting both one-to-one and one-to-many ortholog relationships and filtering them based on their reliability.
+
+**Discovering Paralogs:** In the same vein, *RNAlysis* now facilitates the discovery of paralogs within a specific organism, using either the Ensembl or Panther databases.
+
+**New visualization and analysis options for Principal Component Analysis (PCA):** We've introduced new functions and parameters to allow you to get more out of your principal component analysis.
+
+I would also like to extend my personal apology for the delay in bringing you this update.
+Due to personal reasons, this release, originally scheduled for the end of August, took longer than expected.
+Your patience and support have been invaluable, and I'm eager to share these exciting additions with you.
+Thank you for being a part of the RNAlysis community, and stay tuned for more updates in the near future!
+
+Added
+*******
+* Added new functions to the filtering module that map genes to their closest orthologs in a different organism, using four different databases: Ensembl, Panther, PhylomeDB, and OrthoInspector.
+* Added new functions to the filtering module that find paralogs of genes in a given organism, using two different databases: Ensembl and Panther.
+* Added new function 'Sort table by contribution to a Principal Component (PCA)' (CountFilter.sort_by_principal_component), which allows sorting of genes in a count matrix by their contribution (gene loadings) to a principal component.
+* Added a new parameter called 'legend' to 'Principal Component Analysis (PCA) plot' (CountFilter.pca), which allows users to display a legend on the PCA plot with a name for each sample group/color.
+
+Changed
+********
+* RNAlysis now issues a warning when users run PCA or PCA-based functions on an unnormalized count matrix.
+* The 'seek_fusion_genes' and 'learn_bias' arguments for kallisto quantification (fastq.kallisto_quant_single_end and fastq.kallisto_quant_paired_end), which were depracated in kallisto versions >0.48, are no longer displayed on the graphical interface. Old Pipelines that contain these arguments will still run, but new Pipelines will not contain them.
+
+Fixed
+*******
+* Fixed bug where functions would sometimes fail to run without displaying an error message.
+* Fixed bug where progress bars in the graphical interface would sometimes not disappear after reaching 100% completion.
+* RNAlysis should no longer display warning messages about graph layout when graphs are scaled down.
+* Fixed bug where the clustergram function (CountFilter.clustergram) would raise an error with specific sets of dependecy versions.
+* Loading tables no longer raises a depracation warning when using newer versions of Pandas.
+
 3.9.2 (2023-06-23)
 ------------------
 This patch contains bug fixes and improved functionality for enrichment lollipop plots,

Makefile

@@ -80,7 +80,7 @@ release: dist ## package and upload a release
 	twine upload dist/*
 
 dist: clean ## builds source and wheel package
-	python setup.py sdist
+	python setup.py sdist bdist_wheel
 	python setup.py bdist_wheel
 	ls -l dist
 

RNAlysis.spec

@@ -90,5 +90,5 @@ if not is_darwin:
         strip=False,
         upx=True,
         upx_exclude=[],
-        name='RNAlysis-3.9.2',
+        name='RNAlysis-3.10.0',
     )

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: 4f79531dc52f23f438fcc8023850d20a
+config: 181252bb397a98d0e836b8bbf9c8cf8a
 tags: 645f666f9bcd5a90fca523b33c5a78b7

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.find\_paralogs\_ensembl
+======================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.find_paralogs_ensembl

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.find\_paralogs\_panther
+======================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.find_paralogs_panther

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.map\_orthologs\_ensembl
+======================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.map_orthologs_ensembl

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.map\_orthologs\_orthoinspector
+=============================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.map_orthologs_orthoinspector

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.map\_orthologs\_panther
+======================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.map_orthologs_panther

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.map\_orthologs\_phylomedb
+========================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.map_orthologs_phylomedb

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

@@ -1,4 +1,4 @@
-rnalysis.filtering.CountFilter
+rnalysis.filtering.CountFilter
 ==============================
 
 .. currentmodule:: rnalysis.filtering
@@ -39,6 +39,8 @@ rnalysis.filtering.CountFilter
     CountFilter.filter_missing_values
     CountFilter.filter_percentile
     CountFilter.filter_top_n
+    CountFilter.find_paralogs_ensembl
+    CountFilter.find_paralogs_panther
     CountFilter.fold_change
     CountFilter.from_dataframe
     CountFilter.from_folder
@@ -47,6 +49,10 @@ rnalysis.filtering.CountFilter
     CountFilter.intersection
     CountFilter.ma_plot
     CountFilter.majority_vote_intersection
+    CountFilter.map_orthologs_ensembl
+    CountFilter.map_orthologs_orthoinspector
+    CountFilter.map_orthologs_panther
+    CountFilter.map_orthologs_phylomedb
     CountFilter.normalize_median_of_ratios
     CountFilter.normalize_rle
     CountFilter.normalize_tmm
@@ -66,6 +72,7 @@ rnalysis.filtering.CountFilter
     CountFilter.save_table
     CountFilter.scatter_sample_vs_sample
     CountFilter.sort
+    CountFilter.sort_by_principal_component
     CountFilter.split_by_attribute
     CountFilter.split_by_percentile
     CountFilter.split_by_principal_components

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.sort\_by\_principal\_component
+=============================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.sort_by_principal_component

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.DESeqFilter.find\_paralogs\_ensembl
+======================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: DESeqFilter.find_paralogs_ensembl

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.DESeqFilter.find\_paralogs\_panther
+======================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: DESeqFilter.find_paralogs_panther

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.DESeqFilter.map\_orthologs\_ensembl
+======================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: DESeqFilter.map_orthologs_ensembl

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.DESeqFilter.map\_orthologs\_orthoinspector
+=============================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: DESeqFilter.map_orthologs_orthoinspector

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.DESeqFilter.map\_orthologs\_panther
+======================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: DESeqFilter.map_orthologs_panther

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.DESeqFilter.map\_orthologs\_phylomedb
+========================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: DESeqFilter.map_orthologs_phylomedb

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

@@ -1,4 +1,4 @@
-rnalysis.filtering.DESeqFilter
+rnalysis.filtering.DESeqFilter
 ==============================
 
 .. currentmodule:: rnalysis.filtering
@@ -34,10 +34,16 @@ rnalysis.filtering.DESeqFilter
     DESeqFilter.filter_percentile
     DESeqFilter.filter_significant
     DESeqFilter.filter_top_n
+    DESeqFilter.find_paralogs_ensembl
+    DESeqFilter.find_paralogs_panther
     DESeqFilter.from_dataframe
     DESeqFilter.head
     DESeqFilter.intersection
     DESeqFilter.majority_vote_intersection
+    DESeqFilter.map_orthologs_ensembl
+    DESeqFilter.map_orthologs_orthoinspector
+    DESeqFilter.map_orthologs_panther
+    DESeqFilter.map_orthologs_phylomedb
     DESeqFilter.number_filters
     DESeqFilter.print_features
     DESeqFilter.save_csv

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.Filter.find\_paralogs\_ensembl
+=================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: Filter.find_paralogs_ensembl

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.Filter.find\_paralogs\_panther
+=================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: Filter.find_paralogs_panther

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.Filter.map\_orthologs\_ensembl
+=================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: Filter.map_orthologs_ensembl

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.Filter.map\_orthologs\_orthoinspector
+========================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: Filter.map_orthologs_orthoinspector

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.Filter.map\_orthologs\_panther
+=================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: Filter.map_orthologs_panther

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.Filter.map\_orthologs\_phylomedb
+===================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: Filter.map_orthologs_phylomedb

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

@@ -1,4 +1,4 @@
-rnalysis.filtering.Filter
+rnalysis.filtering.Filter
 =========================
 
 .. currentmodule:: rnalysis.filtering
@@ -31,10 +31,16 @@ rnalysis.filtering.Filter
     Filter.filter_missing_values
     Filter.filter_percentile
     Filter.filter_top_n
+    Filter.find_paralogs_ensembl
+    Filter.find_paralogs_panther
     Filter.from_dataframe
     Filter.head
     Filter.intersection
     Filter.majority_vote_intersection
+    Filter.map_orthologs_ensembl
+    Filter.map_orthologs_orthoinspector
+    Filter.map_orthologs_panther
+    Filter.map_orthologs_phylomedb
     Filter.number_filters
     Filter.print_features
     Filter.save_csv

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.FoldChangeFilter.find\_paralogs\_ensembl
+===========================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: FoldChangeFilter.find_paralogs_ensembl

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.FoldChangeFilter.find\_paralogs\_panther
+===========================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: FoldChangeFilter.find_paralogs_panther

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.FoldChangeFilter.map\_orthologs\_ensembl
+===========================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: FoldChangeFilter.map_orthologs_ensembl

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

@@ -0,0 +1,6 @@
+rnalysis.filtering.FoldChangeFilter.map\_orthologs\_orthoinspector
+==================================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: FoldChangeFilter.map_orthologs_orthoinspector