Merge branch 'documentation'

# Conflicts:
#	qctoolkit/pulses/sequence_pulse_template.py
#	qctoolkit/pulses/table_pulse_template.py
#	tests/pulses/sequence_pulse_template_tests.py

.gitignore

@@ -5,4 +5,5 @@ doc/build/*
 .eggs*
 *.egg-info*
 build/*
-dist/*
+dist/*
+doc/source/examples/.ipynb_checkpoints/*

MATLAB/qctoolkitExample.m

@@ -35,8 +35,7 @@
 sequencer.push(table_pulse_1, parameters);
 sequencer.push(table_pulse_1, parameters);
 
-block = sequencer.build();
-sequence = block.compile_sequence();
+sequence = sequencer.build();
 
 % Convert the instruction sequence to pulse_control pulses and a
 % pulse_group

doc/Makefile

@@ -6,6 +6,7 @@ SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = build
+SPHINXAPIDOC  = sphinx-apidoc
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
@@ -51,38 +52,41 @@ help:
 clean:
 	rm -rf $(BUILDDIR)/*
 
-html:
+extractapi:
+    $(SPHINXAPIDOC) --no-toc -o source ../qctoolkit
+
+html: extractapi
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
-dirhtml:
+dirhtml: extractapi
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
 
-singlehtml:
+singlehtml: extractapi
 	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
 	@echo
 	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
 
-pickle:
+pickle: extractapi
 	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
 	@echo
 	@echo "Build finished; now you can process the pickle files."
 
-json:
+json: extractapi
 	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
 	@echo
 	@echo "Build finished; now you can process the JSON files."
 
-htmlhelp:
+htmlhelp: extractapi
 	$(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:
+qthelp: extractapi
 	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
@@ -91,15 +95,15 @@ qthelp:
 	@echo "To view the help file:"
 	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/qc-toolkit.qhc"
 
-applehelp:
+applehelp: extractapi
 	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
 	@echo
 	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
 	@echo "N.B. You won't be able to view it unless you put it in" \
 	      "~/Library/Documentation/Help or install it in your application" \
 	      "bundle."
 
-devhelp:
+devhelp: extractapi
 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
 	@echo
 	@echo "Build finished."
@@ -108,85 +112,85 @@ devhelp:
 	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/qc-toolkit"
 	@echo "# devhelp"
 
-epub:
+epub: extractapi
 	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
 	@echo
 	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
 
-latex:
+latex: extractapi
 	$(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:
+latexpdf: extractapi
 	$(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."
 
-latexpdfja:
+latexpdfja: extractapi
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo "Running LaTeX files through platex and dvipdfmx..."
 	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
 	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
 
-text:
+text: extractapi
 	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
 	@echo
 	@echo "Build finished. The text files are in $(BUILDDIR)/text."
 
-man:
+man: extractapi
 	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
 	@echo
 	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
 
-texinfo:
+texinfo: extractapi
 	$(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:
+info: extractapi
 	$(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:
+gettext: extractapi
 	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
 	@echo
 	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
 
-changes:
+changes: extractapi
 	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
 	@echo
 	@echo "The overview file is in $(BUILDDIR)/changes."
 
-linkcheck:
+linkcheck: extractapi
 	$(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:
+doctest: extractapi
 	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
 	@echo "Testing of doctests in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/doctest/output.txt."
 
-coverage:
+coverage: extractapi
 	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
 	@echo "Testing of coverage in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/coverage/python.txt."
 
-xml:
+xml: extractapi
 	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
 	@echo
 	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
 
-pseudoxml:
+pseudoxml: extractapi
 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
 	@echo
 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

doc/README.md

@@ -0,0 +1,14 @@
+# qc-toolkit: Quantum Computing Toolkit - Documentation
+
+This folder contains texts, configuration and scripts which are used to compile the documentation using [sphinx](http://www.sphinx-doc.org/en/stable/). It also contains usage examples for the qctoolkit.
+You may either build the documentation yourself or read it on [readthedocs](http://qc-toolkit.readthedocs.org/).[![Documentation Status](https://readthedocs.org/projects/qc-toolkit/badge/?version=latest)](http://qc-toolkit.readthedocs.org/en/latest/?badge=latest)
+
+
+## Examples
+In the subdirectory *examples* you can find various [Jupyter notebook](http://jupyter.org/) files providing some step-by-step examples of how the qctoolkit can be used. These can be explored in an interactive fashion by running the *Jupyter notebook* application inside the folder. However, a static version will also be included in the documentation created with *sphinx*.
+
+## Building the Documentation
+To build the documentation, you will need [sphinx](http://www.sphinx-doc.org/en/stable/) and [nbsphinx](https://nbsphinx.readthedocs.org/) which, in turn, requires [pandoc](http://pandoc.org/). If the last two are not present, the examples won't be included in the documentation.
+Users of Anaconda on MS Windows may install these by executing `pip install sphinx nbsphinx` and `conda install -c https://conda.binstar.org/asmeurer pandoc`.
+
+The documentation is built by invoking `make <format>` inside the */doc* directory, where `<format>` is an output format supported by *sphinx*, e.g., `html`. The output will then be found in `/doc/build/<target>`.

doc/make.bat

@@ -71,6 +71,7 @@ if errorlevel 9009 (
 
 :sphinx_ok
 
+sphinx-apidoc --no-toc -o source ../qctoolkit
 
 if "%1" == "html" (
 	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html

doc/requirements.txt

@@ -0,0 +1,3 @@
+sphinx>=1.4
+nbsphinx
+ipykernel

doc/source/concepts/branching.rst

@@ -0,0 +1,12 @@
+.. _branching:
+
+Conditional Branching
+---------------------
+
+The qctoolkit was designed to model conditional branching in pulse execution using the classes :class:`.BranchPulseTemplate` and :class:`.LoopPulseTemplate` of the :ref:`pulse template definition classes <pulsetemplates>`. The software is intended to support use of trigger-based hardware jumps between waveforms as well as software-based evaluation of branching conditions, if the hardware does not support triggers or highly sophisticated evaluation of measured data is required. These options are represented as instances of the :class:`.Condition` class: :class:`.BranchPulseTemplate` and :class:`.LoopPulseTemplate` both contain unique identifiers (chosen by the user) of a condition. In the beginning of the :ref:`sequencing process <sequencing>`, the user provides a dictionary of :class:`.Condition` instances which are used to determine how the conditions for each template are evaluated. Currently, two different subclasses of :class:`.Condition` exist: :class:`.SoftwareCondition` represents a software-evaluated condition and accepts a function reference to any evaluation function which must return a boolean value indicating whether or not the condition is fulfilled or None, if it cannot yet be evaluated; :class:`.HardwareCondition` represents trigger-based hardware evaluation and basically stores a reference to a trigger which will later be evaluated by the specific hardware driver to set up the device accordingly. Note that software-based evaluation will interrupt the sequencing process and thus the execution of the pulse if the evaluation cannot be performed during the sequencing run, e.g., if the evaluation of the condition is based on measurement data made during pulse execution. In this case, the pulse instruction sequence is only generated up to the branching and must be re-invoked later on, after executing this first part and obtaining the required data. Software-based evaluation is thus not feasible when high performance is required.
+
+Future Work
+^^^^^^^^^^^
+Currently, there is no detailed concept on hardware abstraction and thus no meaningful representation of triggers and no hardware driver implementation that configures any device. This is still an open task.
+
+It is quite common for hardware to allow triggers that are represented not only a boolean signal but, e.g., any 8-bit signal, thus enabling more than two branching options. While this could still be represented by the current classes by nesting :class:`.BranchPulseTemplate` objects and configuring triggers appropriately, the implementation of a template class which acts like a C-style switch statement might be a worthwhile consideration.

doc/source/concepts/concepts.rst

@@ -0,0 +1,10 @@
+Concepts
+========
+
+This section will explain the fundamental design concepts of the qctoolkit.
+
+.. toctree::
+    pulsetemplates
+    serialization
+    branching
+    sequencing