Major changes to main_dev

.gitignore

@@ -15,12 +15,10 @@
 *.tar.*
 *.egg*
 *.tmproj
-*.png
 *.idea
 *.old
 *.dat
 *.bak
-test_*.py
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -35,7 +33,6 @@ old/
 devel
 env/
 bin/
-build/
 develop-eggs/
 dist/
 eggs/
@@ -76,6 +73,10 @@ coverage.xml
 *.pot
 
 # Sphinx documentation
-docs/_build/
+.buildinfo
+.doctrees/
 
 .DS_Store
+.ipynb_checkpoints/
+
+*.label

Makefile

@@ -0,0 +1,61 @@
+# simple makefile to simplify repetitive build env management tasks under posix
+# taken from Makefile for mne-python and adapted for jumeg
+
+PYTHON ?= python
+PYTESTS ?= py.test
+CTAGS ?= ctags
+CODESPELL_SKIPS ?= "doc/_build,doc/auto_*,*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg,references.bib,*.css,*.edf,*.bdf,*.vhdr"
+CODESPELL_DIRS ?= jumeg/ doc/ examples/
+all: clean inplace test test-doc
+
+clean-pyc:
+	find . -name "*.pyc" | xargs rm -f
+
+clean-so:
+	find . -name "*.so" | xargs rm -f
+	find . -name "*.pyd" | xargs rm -f
+
+clean-build:
+	rm -rf build dist
+
+clean-ctags:
+	rm -f tags
+
+clean-cache:
+	find . -name "__pycache__" | xargs rm -rf
+
+clean: clean-build clean-pyc clean-so clean-ctags clean-cache
+
+in: inplace # just a shortcut
+inplace:
+	$(PYTHON) setup.py build_ext -i
+
+wheel:
+	$(PYTHON) setup.py sdist bdist_wheel
+
+wheel_quiet:
+	$(PYTHON) setup.py -q sdist bdist_wheel
+
+pytest: test
+
+test: in
+	rm -f .coverage
+	$(PYTESTS) -m 'not ultraslowtest' jumeg
+
+test-verbose: in
+	rm -f .coverage
+	$(PYTESTS) -m 'not ultraslowtest' jumeg --verbose
+
+test-fast: in
+	rm -f .coverage
+	$(PYTESTS) -m 'not slowtest' jumeg
+
+test-full: in
+	rm -f .coverage
+	$(PYTESTS) jumeg
+
+build-doc:
+	cd docs; make clean
+	# cd docs; DISPLAY=:1.0 xvfb-run -n 1 -s "-screen 0 1280x1024x24 -noreset -ac +extension GLX +render" make html
+	cd docs; make html
+

docs/Makefile

@@ -0,0 +1,188 @@
+# makefile for Sphinx documentation
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = build
+
+GITHUB_PAGES_BRANCH = jumeg_sphinx
+OUTPUTDIR = build/html
+
+# Put it first so that "make" without argument is like "make help".
+# help:
+# 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+# 
+# .PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  clean      to remove genrated output"
+	@echo "  html       to make standalone HTML files"
+	@echo "  notebooks  to make the Jupyter notebook-based tutorials"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+	-rm -rf auto_examples/*
+	-rm -rf generated/*
+
+# tutorials:
+# 	make -C tutorial
+# 
+# introduction: introduction.ipynb
+# 	tools/nb_to_doc.py introduction
+
+# notebooks: tutorials introduction
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/lyman.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/lyman.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/lyman"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/lyman"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+install:
+	touch $(BUILDDIR)/.nojekyll
+	git add $(BUILDDIR)/.nojekyll
+	rm -rf ./auto_examples ./generated
+	mv $(OUTPUTDIR)/* ./
+	rm -rf ./$(BUILDDIR)/
+	git commit -a -m 'Generate jumeg site' ./$(SOURCEDIR)
+	git push origin $(GITHUB_PAGES_BRANCH)

docs/api.rst

@@ -0,0 +1,49 @@
+.. _api_documentation:
+
+=================
+API Documentation
+=================
+
+.. currentmodule:: jumeg
+
+Connectivity
+============
+
+Functions
+
+.. currentmodule:: jumeg.connectivity
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+    find_distances_matrix
+    weighted_con_matrix
+    get_label_distances
+    make_annot_from_csv
+
+    sensor_connectivity_3d
+    plot_grouped_connectivity_circle
+    plot_generic_grouped_circle
+    plot_grouped_causality_circle
+    plot_degree_circle
+    plot_lines_and_blobs
+    plot_labelled_group_connectivity_circle
+    plot_fica_grouped_circle
+
+.. currentmodule:: jumeg.connectivity.causality
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+    dw_whiteness
+    consistency
+    do_mvar_evaluation
+    check_whiteness_and_consistency
+    check_model_order
+    prepare_causality_matrix
+    make_frequency_bands
+    compute_order_extended
+    compute_order
+    compute_causal_outflow_inflow