updated docs for V3.9.0

GuyTeichman · Jun 9, 2023 · 1280eec · 1280eec
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -13,13 +13,13 @@ and addresses multiple bug fixes, including issues with automatic session report
 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 new parameter to Principal Component Analysis plots (CountFilter.pca) 'plot_grid', which can enable or disable adding a grid to PCA plots.
+* 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 report.
+* 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.

diff --git a/docs/build/.buildinfo b/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
diff --git a/docs/build/.doctrees/api_reference.doctree b/docs/build/.doctrees/api_reference.doctree
diff --git a/docs/build/.doctrees/environment.pickle b/docs/build/.doctrees/environment.pickle
diff --git a/docs/build/.doctrees/history.doctree b/docs/build/.doctrees/history.doctree
diff --git a/docs/build/.doctrees/index.doctree b/docs/build/.doctrees/index.doctree
diff --git a/docs/build/.doctrees/readme.doctree b/docs/build/.doctrees/readme.doctree
diff --git a/docs/build/.doctrees/rnalysis.doctree b/docs/build/.doctrees/rnalysis.doctree
diff --git a/docs/build/.doctrees/rnalysis.enrichment.FeatureSet.go_enrichment.doctree b/docs/build/.doctrees/rnalysis.enrichment.FeatureSet.go_enrichment.doctree
diff --git a/docs/build/.doctrees/rnalysis.enrichment.FeatureSet.kegg_enrichment.doctree b/docs/build/.doctrees/rnalysis.enrichment.FeatureSet.kegg_enrichment.doctree
diff --git a/docs/build/.doctrees/rnalysis.enrichment.FeatureSet.user_defined_enrichment.doctree b/docs/build/.doctrees/rnalysis.enrichment.FeatureSet.user_defined_enrichment.doctree
diff --git a/docs/build/.doctrees/rnalysis.enrichment.RankedSet.go_enrichment.doctree b/docs/build/.doctrees/rnalysis.enrichment.RankedSet.go_enrichment.doctree
diff --git a/docs/build/.doctrees/rnalysis.enrichment.RankedSet.kegg_enrichment.doctree b/docs/build/.doctrees/rnalysis.enrichment.RankedSet.kegg_enrichment.doctree
diff --git a/docs/build/.doctrees/rnalysis.enrichment.RankedSet.single_set_enrichment.doctree b/docs/build/.doctrees/rnalysis.enrichment.RankedSet.single_set_enrichment.doctree
diff --git a/docs/build/.doctrees/rnalysis.enrichment.RankedSet.single_set_go_enrichment.doctree b/docs/build/.doctrees/rnalysis.enrichment.RankedSet.single_set_go_enrichment.doctree
diff --git a/docs/build/.doctrees/rnalysis.enrichment.RankedSet.single_set_kegg_enrichment.doctree b/docs/build/.doctrees/rnalysis.enrichment.RankedSet.single_set_kegg_enrichment.doctree
diff --git a/docs/build/.doctrees/rnalysis.enrichment.RankedSet.user_defined_enrichment.doctree b/docs/build/.doctrees/rnalysis.enrichment.RankedSet.user_defined_enrichment.doctree
diff --git a/docs/build/.doctrees/rnalysis.enrichment.enrichment_bar_plot.doctree b/docs/build/.doctrees/rnalysis.enrichment.enrichment_bar_plot.doctree
diff --git a/docs/build/.doctrees/rnalysis.fastq.PairedEndPipeline.doctree b/docs/build/.doctrees/rnalysis.fastq.PairedEndPipeline.doctree
diff --git a/docs/build/.doctrees/rnalysis.fastq.SingleEndPipeline.doctree b/docs/build/.doctrees/rnalysis.fastq.SingleEndPipeline.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.CountFilter.doctree b/docs/build/.doctrees/rnalysis.filtering.CountFilter.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.CountFilter.pca.doctree b/docs/build/.doctrees/rnalysis.filtering.CountFilter.pca.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.CountFilter.save_parquet.doctree b/docs/build/.doctrees/rnalysis.filtering.CountFilter.save_parquet.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.CountFilter.save_table.doctree b/docs/build/.doctrees/rnalysis.filtering.CountFilter.save_table.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.DESeqFilter.doctree b/docs/build/.doctrees/rnalysis.filtering.DESeqFilter.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.DESeqFilter.save_parquet.doctree b/docs/build/.doctrees/rnalysis.filtering.DESeqFilter.save_parquet.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.DESeqFilter.save_table.doctree b/docs/build/.doctrees/rnalysis.filtering.DESeqFilter.save_table.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.Filter.doctree b/docs/build/.doctrees/rnalysis.filtering.Filter.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.Filter.save_parquet.doctree b/docs/build/.doctrees/rnalysis.filtering.Filter.save_parquet.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.Filter.save_table.doctree b/docs/build/.doctrees/rnalysis.filtering.Filter.save_table.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.FoldChangeFilter.doctree b/docs/build/.doctrees/rnalysis.filtering.FoldChangeFilter.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.FoldChangeFilter.save_parquet.doctree b/docs/build/.doctrees/rnalysis.filtering.FoldChangeFilter.save_parquet.doctree
diff --git a/docs/build/.doctrees/rnalysis.filtering.FoldChangeFilter.save_table.doctree b/docs/build/.doctrees/rnalysis.filtering.FoldChangeFilter.save_table.doctree
diff --git a/docs/build/.doctrees/tutorial.doctree b/docs/build/.doctrees/tutorial.doctree
diff --git a/docs/build/_sources/rnalysis.filtering.CountFilter.rst.txt b/docs/build/_sources/rnalysis.filtering.CountFilter.rst.txt
@@ -1,4 +1,4 @@
-rnalysis.filtering.CountFilter
+rnalysis.filtering.CountFilter
 ==============================
 
 .. currentmodule:: rnalysis.filtering
@@ -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

diff --git a/docs/build/_sources/rnalysis.filtering.CountFilter.save_parquet.rst.txt b/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
diff --git a/docs/build/_sources/rnalysis.filtering.CountFilter.save_table.rst.txt b/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
diff --git a/docs/build/_sources/rnalysis.filtering.DESeqFilter.rst.txt b/docs/build/_sources/rnalysis.filtering.DESeqFilter.rst.txt
@@ -1,4 +1,4 @@
-rnalysis.filtering.DESeqFilter
+rnalysis.filtering.DESeqFilter
 ==============================
 
 .. currentmodule:: rnalysis.filtering
@@ -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

diff --git a/docs/build/_sources/rnalysis.filtering.DESeqFilter.save_parquet.rst.txt b/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
diff --git a/docs/build/_sources/rnalysis.filtering.DESeqFilter.save_table.rst.txt b/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
diff --git a/docs/build/_sources/rnalysis.filtering.Filter.rst.txt b/docs/build/_sources/rnalysis.filtering.Filter.rst.txt
@@ -1,4 +1,4 @@
-rnalysis.filtering.Filter
+rnalysis.filtering.Filter
 =========================
 
 .. currentmodule:: rnalysis.filtering
@@ -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

diff --git a/docs/build/_sources/rnalysis.filtering.Filter.save_parquet.rst.txt b/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
diff --git a/docs/build/_sources/rnalysis.filtering.Filter.save_table.rst.txt b/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
diff --git a/docs/build/_sources/rnalysis.filtering.FoldChangeFilter.rst.txt b/docs/build/_sources/rnalysis.filtering.FoldChangeFilter.rst.txt
@@ -1,4 +1,4 @@
-rnalysis.filtering.FoldChangeFilter
+rnalysis.filtering.FoldChangeFilter
 ===================================
 
 .. currentmodule:: rnalysis.filtering
@@ -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

diff --git a/docs/build/_sources/rnalysis.filtering.FoldChangeFilter.save_parquet.rst.txt b/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
diff --git a/docs/build/_sources/rnalysis.filtering.FoldChangeFilter.save_table.rst.txt b/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
diff --git a/docs/build/_static/documentation_options.js b/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',