Merge rc into main. (#8)

* moved get_gem_data within the Interface class.

* minor updates, transfering work

* merging changes..

* updated plotting functions.

* bug fixes, travis_dev

* bug fixes

* current work for remote

* updated samplewise plots and notebooks

* code updates, machine transfer

* new notebooks

* updates and transfer

* bugs squashed, notebooks updated, travis_dev

* changed dockerfile pip install to user.

* updated gitignore, travis_dev

* updated dockerfile, travis_dev

* fixed missing -p in mkdir of dockerfile.

* docker file permission woes, travis_dev

* more docker fixes, travis_dev

* more docker woes, travis_dev

* changed to python 3.7 in docker image

* docker test, travis_dev

* docker fixed? travis_dev

* more docker fixes, travis_dev

* moving code

* prep for release tag

* rc prep, travis_dev

* added upsetplot to requirements, travis_dev

* removed "offset" command from nbsite command, travis_dev

* minor fixes, travis_dev

* doc reorg push

* documentation updates

* docs working locally

* doc updates

* more minor doc fixes, travis_dev

* updated docs install requirements, travis_dev

* added kernelspec definition to travis.yml, travis_dev

* fixed more travis.yml stuff, travis_dev

* removed example copy from dockerfile, travis_dev

* conf.py fix for readthedocs theme, travis_dev

* removed underscores from docs folders for github pages, travis_dev

* added a .nojekyll for GH-pages

* same, travis_dev

* now with the dev process, travis_dev

* fixed filepaths in travis.yml for nojekyll, travis_dev

* fixed same error for release deploy

* minor fixes and doc updates

* refactored GeneSet get_n_top_genes into separate funcs

* doc updates, travis_dev

* nf prep, travis_dev

* travis_dev

* nf config profile added

* repaired analytics

* updated boruta multiclass script

* go travs? travis_dev

* doc updates, travis_dev

* docs updated, travis_dev

* tour run updated

* walkthrough notebooks ran

* updated docs, travis_dev

* doc updates, travis_dev

* fixed filepahths, travis_dev

* Removed notebook cache.

* Removed notebook cache. travis_dev

* go travis_dev

* go travis_dev

* removed notebooks from travis running

* refactored docs, travis_dev

* Updated documentation. Local docs building via docker.

* Refactored gene_support to get_support.

* Prep master merge. travis_dev

* Prep master merge again. travis_dev

* Added package versions. travis_dev

Co-authored-by: root <root@MSI.localdomain>

.dockerignore

@@ -1,110 +1,110 @@
-# The dockerfile has trouble installing GSForge from development machines
-# if this file is not complete. It gives strange permission errors.
-
-# Git
-.git
-.gitignore
-
-# CI
-.codeclimate.yml
-.travis.yml
-.taskcluster.yml
-
-# Docker
-docker-compose.yml
-.docker
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*/__pycache__/
-*/*/__pycache__/
-*/*/*/__pycache__/
-*.py[cod]
-*/*.py[cod]
-*/*/*.py[cod]
-*/*/*/*.py[cod]
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.cache
-nosetests.xml
-coverage.xml
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Virtual environment
-.env/
-.venv/
-venv/
-
-# PyCharm
-.idea
-
-# Python mode for VIM
-.ropeproject
-*/.ropeproject
-*/*/.ropeproject
-*/*/*/.ropeproject
-
-# Vim swap files
-*.swp
-*/*.swp
-*/*/*.swp
-*/*/*/*.swp
-
-
-# Jupyter lab
-.ipynb_checkpoints
-binder/
-tests/
-docker/
-workflows/
-
-# Datafiles
-*.nc
-*/*.nc
-*/*/*.nc
-*/*/*/*.nc
+# The dockerfile has trouble installing GSForge from development machines
+# if this file is not complete. It gives strange permission errors.
+
+# Git
+.git
+.gitignore
+
+# CI
+.codeclimate.yml
+.travis.yml
+.taskcluster.yml
+
+# Docker
+docker-compose.yml
+.docker
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*/__pycache__/
+*/*/__pycache__/
+*/*/*/__pycache__/
+*.py[cod]
+*/*.py[cod]
+*/*/*.py[cod]
+*/*/*/*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Virtual environment
+.env/
+.venv/
+venv/
+
+# PyCharm
+.idea
+
+# Python mode for VIM
+.ropeproject
+*/.ropeproject
+*/*/.ropeproject
+*/*/*/.ropeproject
+
+# Vim swap files
+*.swp
+*/*.swp
+*/*/*.swp
+*/*/*/*.swp
+
+
+# Jupyter lab
+.ipynb_checkpoints
+binder/
+tests/
+docker/
+workflows/
+
+# Datafiles
+*.nc
+*/*.nc
+*/*/*.nc
+*/*/*/*.nc