Merge remote-tracking branch 'origin/development'

# Conflicts: # .bumpversion.cfg # HISTORY.rst # README.rst # docs/build/.buildinfo # docs/build/.doctrees/api_reference.doctree # docs/build/.doctrees/environment.pickle # docs/build/.doctrees/history.doctree # docs/build/.doctrees/index.doctree # docs/build/.doctrees/readme.doctree # docs/build/.doctrees/rnalysis.doctree # docs/build/.doctrees/rnalysis.enrichment.FeatureSet.doctree # docs/build/.doctrees/rnalysis.enrichment.FeatureSet.enrich_hypergeometric.doctree # docs/build/.doctrees/rnalysis.enrichment.FeatureSet.enrich_randomization.doctree # docs/build/.doctrees/rnalysis.enrichment.FeatureSet.enrich_randomization_parallel.doctree # docs/build/.doctrees/rnalysis.enrichment.FeatureSet.go_enrichment.doctree # docs/build/.doctrees/rnalysis.enrichment.FeatureSet.non_categorical_enrichment.doctree # docs/build/.doctrees/rnalysis.enrichment.RankedSet.doctree # docs/build/.doctrees/rnalysis.enrichment.RankedSet.enrich_hypergeometric.doctree # docs/build/.doctrees/rnalysis.enrichment.RankedSet.enrich_randomization.doctree # docs/build/.doctrees/rnalysis.enrichment.RankedSet.enrich_randomization_parallel.doctree # docs/build/.doctrees/rnalysis.enrichment.RankedSet.go_enrichment.doctree # docs/build/.doctrees/rnalysis.enrichment.RankedSet.non_categorical_enrichment.doctree # docs/build/.doctrees/rnalysis.enrichment.RankedSet.single_set_go_enrichment.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.box_plot.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.clustergram.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.describe.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.difference.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.enhanced_box_plot.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.filter_by_attribute.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.intersection.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.majority_vote_intersection.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.number_filters.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.pca.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.split_by_attribute.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.split_clicom.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.split_hdbscan.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.split_hierarchical.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.split_kmeans.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.split_kmedoids.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.symmetric_difference.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.text_filters.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.union.doctree # docs/build/.doctrees/rnalysis.filtering.CountFilter.violin_plot.doctree # docs/build/.doctrees/rnalysis.filtering.DESeqFilter.describe.doctree # docs/build/.doctrees/rnalysis.filtering.DESeqFilter.difference.doctree # 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docs/build/rnalysis.general.set_biotype_ref_table_path.html # docs/build/rnalysis.html # docs/build/search.html # docs/build/searchindex.js # docs/build/user_guide.html # docs/source/conf.py # requirements.txt # rnalysis/__init__.py # rnalysis/enrichment.py # rnalysis/filtering.py # rnalysis/utils/enrichment_runner.py # rnalysis/utils/io.py # rnalysis/utils/uniprot_dataset_abbreviation_dict.json # setup.py # tests/test_enrichment_runner.py # tests/test_io.py
GuyTeichman · Oct 10, 2022 · 986d285 · 986d285
2 parents 2e5e14a + fa27dd9
commit 986d285
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Showing 560 changed files with 107,635 additions and 3,317 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.1.1
+current_version = 3.0.0
 commit = True
 tag = False
 

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -1,6 +1,6 @@
 name: Build CI
 
-on: [ push ]
+on: [push, pull_request]
 
 jobs:
     build:
@@ -9,11 +9,16 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                os: [ ubuntu-latest, windows-latest, macos-latest ]
+                os: [ubuntu-latest, windows-latest]
                 python-version: [3.7, 3.8]
 
+        env:
+            DISPLAY: ':99.0'
         steps:
-            -   uses: actions/checkout@v2
+            -   name: Get repository
+                uses: actions/checkout@v2
+            -   name: Setup Qt requirements for Linux
+                uses: tlambert03/setup-qt-libs@v1
             -   name: Setup Graphviz
                 uses: ts-graphviz/setup-graphviz@v1
             -   name: Install LLVM and Clang
@@ -25,11 +30,12 @@ jobs:
                 uses: actions/setup-python@v2
                 with:
                     python-version: ${{ matrix.python-version }}
+                    cache: 'pip'
             -   name: Install dependencies
                 run: |
                     python -m pip install --upgrade pip
-                    python -m pip install coverage coveralls pytest
-                    pip install .
+                    python -m pip install coverage coveralls pytest pytest-qt pytest-xvfb
+                    pip install .[all]
             -   name: Test with pytest
                 run: |
                     coverage run --source=rnalysis/ -m pytest tests/

diff --git a/.gitignore b/.gitignore
@@ -114,3 +114,4 @@ settings.ini
 /rnalysis/temp_settings.yaml
 /rnalysis/random_pvals.pyx
 /dask-worker-space/
+/rnalysis/qt6_convert.py
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -102,8 +102,8 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 2.7, 3.4, 3.5 and 3.6, and for PyPy. Check
-   https://travis-ci.org/GuyTeichman/rnalysis/pull_requests
+3. The pull request should work for Python 3.7, 3.8, and for PyPy. Check
+   https://coveralls.io/github/GuyTeichman/RNAlysis
    and make sure that the tests pass for all supported Python versions.
 
 Tips

diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,9 +2,42 @@
 History
 =======
 
+
+
+3.0.0 (2022-10-10)
+------------------
+* This version introduces a graphical user interface for RNAlysis, as well as new functions for KEGG Pathways enrichment analysis.
+
+
+Added
+******
+* RNAlysis now includes a graphical user interface
+* Pipelines can now be imported and exported
+* Enrichment and single-set-enrichment for KEGG pathway data
+
+Changed
+*******
+* Added function FeatureSet.user_defined_enrichment(), which will replace FeatureSet.enrich_hypergeometric() and FeatureSet.enrich_randomization()
+* Updated signature of enrichment.venn_diagram
+* enrichment.venn_diagram and enrichment.upset_plot can now be generated on a user-supplied FIgure
+* Clustering functions now apply a power transform to count data prior to clustering by default
+* Non-deprecated enrichment functions no longer filter the background set by biotype by default
+* Changed signature of CountFilter.pca, CountFilter.box_plot, CountFilter.enhanced_box_plot, CountFilter.clustergram, and CountFilter.pairplot to ensure consistency among visualization functions.
+
+Fixed
+******
+* enrichment.venn_diagram can now be plotted with outlines when the circles are unweighted
+* Fixed bug in Pipeline.apply_to() where a Filter object would be returned even when the Pipeline was applied inplace
+
+Removed
+********
+*
+
+
 2.1.1 (2022-07-05)
 ------------------
-* This version fixes issues with running GO enrichment that resulted from recent changes to UniProt's API. Moreover, this version slightly improves the performance of some functions.
+* This version fixes issues with running GO enrichment that resulted from recent changes to UniProt's API.
+Moreover, this version slightly improves the performance of some functions.
 
 Changed
 *******

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,11 +1,9 @@
-include AUTHORS.rst
-include HISTORY.rst
-include LICENSE
-include README.rst
+recursive-include . *.rst *.ico *.png
 
+recursive-include rnalysis *.png *.webp *.json *.qss *.ico
 
 recursive-include tests *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
-recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif *.ico
diff --git a/README.rst b/README.rst
@@ -12,15 +12,9 @@
 What is *RNAlysis?*
 --------------------
 
-*RNAlysis* is a Python-based modular analysis pipeline for RNA sequencing data.
-You can use it to normalize, filter and visualize your data, cluster genes based on their expression patterns,
-and perform enrichment analysis for both Gene Ontology terms and user-defined attributes.
-
-*RNAlysis* allows you to perform filtering operations and analyses at any order you wish.
-You can save or load your progress at any given point; the operations you performed on your data and their order
-will be reflected in saved file's name.
-
-RNAlysis works with gene expression matrices and differential expression tables in general, and integrates in particular with Python's *HTSeq-count* and R's *DESeq2*.
+*RNAlysis* is a Python-based software for analyzing RNA sequencing data.
+*RNAlysis* allows you to build customized analysis pipelines suiting your specific research questions,
+going all the way from exploratory data analysis and data visualization through clustering analysis and gene-set enrichment analysis.
 
 ----
 
@@ -32,19 +26,45 @@ What can I do with *RNAlysis*?
 * Visualise, explore and describe your sequencing data
 * Find global relationships between sample expression profiles with clustering analyses and dimensionality reduction
 * Create and share analysis pipelines
-* Perform enrichment analysis with pre-determined Gene Ontology terms, or with used-defined attributes
-* Perform enrichment analysis on a single ranked list, instead of a test set and a background set
+* Perform enrichment analysis with pre-determined Gene Ontology terms/KEGG pathways, or with used-defined attributes
+* Perform enrichment analysis on a single ranked list of genes, instead of a test set and a background set
+
+To get an overview of what *RNAlysis* can do, read the `user guide <https://guyteichman.github.io/RNAlysis/build/user_guide.html>`_.
+
+*RNAlysis* supports gene expression matrices and differential expression tables in general, and integrates in particular with Python's *HTSeq-count* and R's *DESeq2*.
 
 ----
 
 How do I install it?
 ---------------------
 You can install *RNAlysis* via PyPI.
-Use the following command in the python prompt::
+To install the basic version of *RNAlysis*, use the following command in your terminal window::
 
     pip install RNAlysis
 
 
+To install the full version of *RNAlysis* (includes additional features that might not work out-of-the-box on all machines), you should first install `GraphViz <https://graphviz.org/download/>`_, and `Microsoft Visual C++ 14.0 <https://visualstudio.microsoft.com/visual-cpp-build-tools/>`_ or greater (on Windows computers only).
+Then use the following command in your terminal window::
+
+    pip install RNAlysis[all]
+
+
+----
+
+
+How do I use it?
+---------------------
+You can launch the *RNAlysis* software by typing the following command::
+
+    rnalysis-gui
+
+Or through a python console::
+
+    >>> from rnalysis import gui
+    >>> gui.run_gui()
+
+Alternatively, you can write Python code that uses *RNAlysis* functions as described in the `user guide <https://guyteichman.github.io/RNAlysis/build/user_guide.html>`_.
+
 ----
 
 Dependencies
@@ -71,6 +91,9 @@ All of *RNAlysis*'s dependencies can be installed automatically via PyPI.
 * `matplotlib-venn <https://github.com/konstantint/matplotlib-venn>`_
 * `xlmhg <https://github.com/flo-compbio/xlmhg>`_
 * `pairwisedist <https://github.com/GuyTeichman/pairwisedist/>`_
+* `typing_extensions <https://github.com/python/typing_extensions>`_
+* `PyQt5 <https://www.riverbankcomputing.com/software/pyqt/>`_
+* `qdarkstyle <https://github.com/ColinDuquesnoy/QDarkStyleSheet>`_
 
 ----
 
@@ -79,7 +102,7 @@ Credits
 
 How do I cite *RNAlysis*?
 **************************
-Teichman, G. (2021) RNAlysis: RNA Sequencing analysis pipeline (Python package version 2.1.1).
+Teichman, G. (2022) RNAlysis: RNA Sequencing analysis software (Python package version 3.0.0).
 
 Development Lead
 ******************

diff --git a/docs/build/.buildinfo b/docs/build/.buildinfo
@@ -1,4 +1,4 @@
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