79 files changed, 660 insertions, 30 deletions
diff --git a/lecture_notes/Makefile b/lecture_notes/Makefile
new file mode 100644
index 0000000..1c06194
--- /dev/null
+++ b/lecture_notes/Makefile
@@ -0,0 +1,153 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.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 "  html       to make standalone HTML files"
+	@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)/*
+
+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/SoftwareEngineeringforEngineersandScientists.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/SoftwareEngineeringforEngineersandScientists.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/SoftwareEngineeringforEngineersandScientists"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/SoftwareEngineeringforEngineersandScientists"
+	@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."
diff --git a/lecture_notes/index.rst b/lecture_notes/index.rst
deleted file mode 100644
index 53edbcc..0000000
--- a/lecture_notes/index.rst
+++ /dev/null
@@ -1,30 +0,0 @@
-.. sees-sphinx documentation master file, created by
-   sphinx-quickstart on Thu Jun  9 18:22:59 2011.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to sees-sphinx's documentation!
-=======================================
-
-Contents:
-
-.. toctree::
-   :maxdepth: 2
-
-   Test 1 <tests/test1>
-   Introduction to the course <introduction/introduction>
-   Using Linux Tools <ult/index.rst>
-   LaTeX <latex/index.rst>
-   Version Control <versionControl/index.rst>
-   Basic Python <basic_python/handOut.rst>
-   Advanced Python <advanced_python/handOut.rst>
-   Test Driven Development <tdd/tdd.rst>
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
diff --git a/lecture_notes/make.bat b/lecture_notes/make.bat
new file mode 100644
index 0000000..bb3ed9c
--- /dev/null
+++ b/lecture_notes/make.bat
@@ -0,0 +1,190 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% source
+set I18NSPHINXOPTS=%SPHINXOPTS% source
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	:help
+	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  html       to make standalone HTML files
+	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.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  texinfo    to make Texinfo files
+	echo.  gettext    to make PO message catalogs
+	echo.  changes    to make an overview over 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
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\SoftwareEngineeringforEngineersandScientists.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\SoftwareEngineeringforEngineersandScientists.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "texinfo" (
+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+	goto end
+)
+
+if "%1" == "gettext" (
+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+:end
diff --git a/lecture_notes/advanced_python/arrays.rst b/lecture_notes/source/advanced_python/arrays.rst
index d5699ce..d5699ce 100644
--- a/lecture_notes/advanced_python/arrays.rst
+++ b/lecture_notes/source/advanced_python/arrays.rst
diff --git a/lecture_notes/advanced_python/data/L_TSq_limited.png b/lecture_notes/source/advanced_python/data/L_TSq_limited.png
index c6e280e..c6e280e 100644
--- a/lecture_notes/advanced_python/data/L_TSq_limited.png
+++ b/lecture_notes/source/advanced_python/data/L_TSq_limited.png
diff --git a/lecture_notes/advanced_python/data/L_Tsq.png b/lecture_notes/source/advanced_python/data/L_Tsq.png
index 75f2c70..75f2c70 100644
--- a/lecture_notes/advanced_python/data/L_Tsq.png
+++ b/lecture_notes/source/advanced_python/data/L_Tsq.png
diff --git a/lecture_notes/advanced_python/data/L_Tsq_Line.png b/lecture_notes/source/advanced_python/data/L_Tsq_Line.png
index 5535eff..5535eff 100644
--- a/lecture_notes/advanced_python/data/L_Tsq_Line.png
+++ b/lecture_notes/source/advanced_python/data/L_Tsq_Line.png
diff --git a/lecture_notes/advanced_python/data/L_Tsq_points.png b/lecture_notes/source/advanced_python/data/L_Tsq_points.png
index 3b8f2a3..3b8f2a3 100644
--- a/lecture_notes/advanced_python/data/L_Tsq_points.png
+++ b/lecture_notes/source/advanced_python/data/L_Tsq_points.png
diff --git a/lecture_notes/advanced_python/data/company_a_data.txt b/lecture_notes/source/advanced_python/data/company_a_data.txt
index 06f4ca4..06f4ca4 100644
--- a/lecture_notes/advanced_python/data/company_a_data.txt
+++ b/lecture_notes/source/advanced_python/data/company_a_data.txt
diff --git a/lecture_notes/advanced_python/data/error_bar.png b/lecture_notes/source/advanced_python/data/error_bar.png
index cc1a454..cc1a454 100644
--- a/lecture_notes/advanced_python/data/error_bar.png
+++ b/lecture_notes/source/advanced_python/data/error_bar.png
diff --git a/lecture_notes/advanced_python/data/least_sq_fit.png b/lecture_notes/source/advanced_python/data/least_sq_fit.png
index dba2afb..dba2afb 100644
--- a/lecture_notes/advanced_python/data/least_sq_fit.png
+++ b/lecture_notes/source/advanced_python/data/least_sq_fit.png
diff --git a/lecture_notes/advanced_python/data/pendulum.txt b/lecture_notes/source/advanced_python/data/pendulum.txt
index 01da9b8..01da9b8 100644
--- a/lecture_notes/advanced_python/data/pendulum.txt
+++ b/lecture_notes/source/advanced_python/data/pendulum.txt
diff --git a/lecture_notes/advanced_python/data/pendulum_error.txt b/lecture_notes/source/advanced_python/data/pendulum_error.txt
index 5cf2194..5cf2194 100644
--- a/lecture_notes/advanced_python/data/pendulum_error.txt
+++ b/lecture_notes/source/advanced_python/data/pendulum_error.txt
diff --git a/lecture_notes/advanced_python/exercises.rst b/lecture_notes/source/advanced_python/exercises.rst
index eeaa323..eeaa323 100644
--- a/lecture_notes/advanced_python/exercises.rst
+++ b/lecture_notes/source/advanced_python/exercises.rst
diff --git a/lecture_notes/advanced_python/handout.rst b/lecture_notes/source/advanced_python/handout.rst
index 2cd3618..2cd3618 100644
--- a/lecture_notes/advanced_python/handout.rst
+++ b/lecture_notes/source/advanced_python/handout.rst
diff --git a/lecture_notes/advanced_python/images/L-Tsq.png b/lecture_notes/source/advanced_python/images/L-Tsq.png
index cc1a454..cc1a454 100644
--- a/lecture_notes/advanced_python/images/L-Tsq.png
+++ b/lecture_notes/source/advanced_python/images/L-Tsq.png
diff --git a/lecture_notes/advanced_python/images/bar.png b/lecture_notes/source/advanced_python/images/bar.png
index cee54fb..cee54fb 100644
--- a/lecture_notes/advanced_python/images/bar.png
+++ b/lecture_notes/source/advanced_python/images/bar.png
diff --git a/lecture_notes/advanced_python/images/cosine.png b/lecture_notes/source/advanced_python/images/cosine.png
index 2b15a32..2b15a32 100644
--- a/lecture_notes/advanced_python/images/cosine.png
+++ b/lecture_notes/source/advanced_python/images/cosine.png
diff --git a/lecture_notes/advanced_python/images/epid.png b/lecture_notes/source/advanced_python/images/epid.png
index e1c7e08..e1c7e08 100644
--- a/lecture_notes/advanced_python/images/epid.png
+++ b/lecture_notes/source/advanced_python/images/epid.png
diff --git a/lecture_notes/advanced_python/images/fsolve.png b/lecture_notes/source/advanced_python/images/fsolve.png
index 0108215..0108215 100644
--- a/lecture_notes/advanced_python/images/fsolve.png
+++ b/lecture_notes/source/advanced_python/images/fsolve.png
diff --git a/lecture_notes/advanced_python/images/loglog.png b/lecture_notes/source/advanced_python/images/loglog.png
index 824b9f1..824b9f1 100644
--- a/lecture_notes/advanced_python/images/loglog.png
+++ b/lecture_notes/source/advanced_python/images/loglog.png
diff --git a/lecture_notes/advanced_python/images/lst-sq-fit.png b/lecture_notes/source/advanced_python/images/lst-sq-fit.png
index 7e9dfe2..7e9dfe2 100644
--- a/lecture_notes/advanced_python/images/lst-sq-fit.png
+++ b/lecture_notes/source/advanced_python/images/lst-sq-fit.png
diff --git a/lecture_notes/advanced_python/images/ode.png b/lecture_notes/source/advanced_python/images/ode.png
index c76a483..c76a483 100644
--- a/lecture_notes/advanced_python/images/ode.png
+++ b/lecture_notes/source/advanced_python/images/ode.png
diff --git a/lecture_notes/advanced_python/images/overlaid.png b/lecture_notes/source/advanced_python/images/overlaid.png
index 41e1891..41e1891 100644
--- a/lecture_notes/advanced_python/images/overlaid.png
+++ b/lecture_notes/source/advanced_python/images/overlaid.png
diff --git a/lecture_notes/advanced_python/images/pie.png b/lecture_notes/source/advanced_python/images/pie.png
index 7791e54..7791e54 100644
--- a/lecture_notes/advanced_python/images/pie.png
+++ b/lecture_notes/source/advanced_python/images/pie.png
diff --git a/lecture_notes/advanced_python/images/plot.png b/lecture_notes/source/advanced_python/images/plot.png
index 89cbc46..89cbc46 100644
--- a/lecture_notes/advanced_python/images/plot.png
+++ b/lecture_notes/source/advanced_python/images/plot.png
diff --git a/lecture_notes/advanced_python/images/roots.png b/lecture_notes/source/advanced_python/images/roots.png
index c13a1a4..c13a1a4 100644
--- a/lecture_notes/advanced_python/images/roots.png
+++ b/lecture_notes/source/advanced_python/images/roots.png
diff --git a/lecture_notes/advanced_python/images/scatter.png b/lecture_notes/source/advanced_python/images/scatter.png
index 66bd5d8..66bd5d8 100644
--- a/lecture_notes/advanced_python/images/scatter.png
+++ b/lecture_notes/source/advanced_python/images/scatter.png
diff --git a/lecture_notes/advanced_python/images/sine.png b/lecture_notes/source/advanced_python/images/sine.png
index 7667886..7667886 100644
--- a/lecture_notes/advanced_python/images/sine.png
+++ b/lecture_notes/source/advanced_python/images/sine.png
diff --git a/lecture_notes/advanced_python/images/slice.png b/lecture_notes/source/advanced_python/images/slice.png
index 7f53d2a..7f53d2a 100644
--- a/lecture_notes/advanced_python/images/slice.png
+++ b/lecture_notes/source/advanced_python/images/slice.png
diff --git a/lecture_notes/advanced_python/images/squares.png b/lecture_notes/source/advanced_python/images/squares.png
index ee102e6..ee102e6 100644
--- a/lecture_notes/advanced_python/images/squares.png
+++ b/lecture_notes/source/advanced_python/images/squares.png
diff --git a/lecture_notes/advanced_python/images/subplot.png b/lecture_notes/source/advanced_python/images/subplot.png
index 2c1a662..2c1a662 100644
--- a/lecture_notes/advanced_python/images/subplot.png
+++ b/lecture_notes/source/advanced_python/images/subplot.png
diff --git a/lecture_notes/advanced_python/lambda.rst b/lecture_notes/source/advanced_python/lambda.rst
index 4660300..4660300 100644
--- a/lecture_notes/advanced_python/lambda.rst
+++ b/lecture_notes/source/advanced_python/lambda.rst
diff --git a/lecture_notes/advanced_python/module_plan.rst b/lecture_notes/source/advanced_python/module_plan.rst
index 2ee4925..2ee4925 100644
--- a/lecture_notes/advanced_python/module_plan.rst
+++ b/lecture_notes/source/advanced_python/module_plan.rst
diff --git a/lecture_notes/advanced_python/modules.rst b/lecture_notes/source/advanced_python/modules.rst
index f3df676..f3df676 100644
--- a/lecture_notes/advanced_python/modules.rst
+++ b/lecture_notes/source/advanced_python/modules.rst
diff --git a/lecture_notes/advanced_python/more_arrays.rst b/lecture_notes/source/advanced_python/more_arrays.rst
index c562edd..c562edd 100644
--- a/lecture_notes/advanced_python/more_arrays.rst
+++ b/lecture_notes/source/advanced_python/more_arrays.rst
diff --git a/lecture_notes/advanced_python/oop.rst b/lecture_notes/source/advanced_python/oop.rst
index b1ecbe8..b1ecbe8 100644
--- a/lecture_notes/advanced_python/oop.rst
+++ b/lecture_notes/source/advanced_python/oop.rst
diff --git a/lecture_notes/advanced_python/plotting.rst b/lecture_notes/source/advanced_python/plotting.rst
index ad246d4..ad246d4 100644
--- a/lecture_notes/advanced_python/plotting.rst
+++ b/lecture_notes/source/advanced_python/plotting.rst
diff --git a/lecture_notes/advanced_python/rst.rst b/lecture_notes/source/advanced_python/rst.rst
index fcbd986..fcbd986 100644
--- a/lecture_notes/advanced_python/rst.rst
+++ b/lecture_notes/source/advanced_python/rst.rst
diff --git a/lecture_notes/advanced_python/sage.rst b/lecture_notes/source/advanced_python/sage.rst
index 46fcef4..46fcef4 100644
--- a/lecture_notes/advanced_python/sage.rst
+++ b/lecture_notes/source/advanced_python/sage.rst
diff --git a/lecture_notes/advanced_python/scipy.rst b/lecture_notes/source/advanced_python/scipy.rst
index fd0508a..fd0508a 100644
--- a/lecture_notes/advanced_python/scipy.rst
+++ b/lecture_notes/source/advanced_python/scipy.rst
diff --git a/lecture_notes/basic_python/exercises.rst b/lecture_notes/source/basic_python/exercises.rst
index 3c02c56..3c02c56 100644
--- a/lecture_notes/basic_python/exercises.rst
+++ b/lecture_notes/source/basic_python/exercises.rst
diff --git a/lecture_notes/basic_python/func.rst b/lecture_notes/source/basic_python/func.rst
index bd9074b..bd9074b 100644
--- a/lecture_notes/basic_python/func.rst
+++ b/lecture_notes/source/basic_python/func.rst
diff --git a/lecture_notes/basic_python/handout.rst b/lecture_notes/source/basic_python/handout.rst
index 37554ab..37554ab 100644
--- a/lecture_notes/basic_python/handout.rst
+++ b/lecture_notes/source/basic_python/handout.rst
diff --git a/lecture_notes/basic_python/intro.rst b/lecture_notes/source/basic_python/intro.rst
index 3953db0..3953db0 100644
--- a/lecture_notes/basic_python/intro.rst
+++ b/lecture_notes/source/basic_python/intro.rst
diff --git a/lecture_notes/basic_python/io_files_parsing.rst b/lecture_notes/source/basic_python/io_files_parsing.rst
index 6bbc2e4..6bbc2e4 100644
--- a/lecture_notes/basic_python/io_files_parsing.rst
+++ b/lecture_notes/source/basic_python/io_files_parsing.rst
diff --git a/lecture_notes/basic_python/module_plan.rst b/lecture_notes/source/basic_python/module_plan.rst
index e4d1cbd..e4d1cbd 100644
--- a/lecture_notes/basic_python/module_plan.rst
+++ b/lecture_notes/source/basic_python/module_plan.rst
diff --git a/lecture_notes/basic_python/strings_loops_lists.rst b/lecture_notes/source/basic_python/strings_loops_lists.rst
index b894f5b..b894f5b 100644
--- a/lecture_notes/basic_python/strings_loops_lists.rst
+++ b/lecture_notes/source/basic_python/strings_loops_lists.rst
diff --git a/lecture_notes/basic_python/tuples_dicts_sets.rst b/lecture_notes/source/basic_python/tuples_dicts_sets.rst
index ff722fd..ff722fd 100644
--- a/lecture_notes/basic_python/tuples_dicts_sets.rst
+++ b/lecture_notes/source/basic_python/tuples_dicts_sets.rst
diff --git a/lecture_notes/source/conf.py b/lecture_notes/source/conf.py
new file mode 100644
index 0000000..174f0df
--- /dev/null
+++ b/lecture_notes/source/conf.py
@@ -0,0 +1,289 @@
+# -*- coding: utf-8 -*-
+#
+# Software Engineering for Engineers and Scientists documentation build configuration file, created by
+# sphinx-quickstart on Fri Jun 13 18:10:23 2014.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Software Engineering for Engineers and Scientists'
+copyright = u'2014, FOSSEE'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '2014'
+# The full version, including alpha/beta/rc tags.
+release = '2014'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'SoftwareEngineeringforEngineersandScientistsdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'SoftwareEngineeringforEngineersandScientists.tex', u'Software Engineering for Engineers and Scientists Documentation',
+   u'FOSSEE', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'softwareengineeringforengineersandscientists', u'Software Engineering for Engineers and Scientists Documentation',
+     [u'FOSSEE'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'SoftwareEngineeringforEngineersandScientists', u'Software Engineering for Engineers and Scientists Documentation',
+   u'FOSSEE', 'SoftwareEngineeringforEngineersandScientists', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+
+# -- Options for Epub output ---------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = u'Software Engineering for Engineers and Scientists'
+epub_author = u'FOSSEE'
+epub_publisher = u'FOSSEE'
+epub_copyright = u'2014, FOSSEE'
+
+# The language of the text. It defaults to the language option
+# or en if the language is not set.
+#epub_language = ''
+
+# The scheme of the identifier. Typical schemes are ISBN or URL.
+#epub_scheme = ''
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#epub_identifier = ''
+
+# A unique identification for the text.
+#epub_uid = ''
+
+# A tuple containing the cover image and cover page html template filenames.
+#epub_cover = ()
+
+# HTML files that should be inserted before the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_pre_files = []
+
+# HTML files shat should be inserted after the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_post_files = []
+
+# A list of files that should not be packed into the epub file.
+#epub_exclude_files = []
+
+# The depth of the table of contents in toc.ncx.
+#epub_tocdepth = 3
+
+# Allow duplicate toc entries.
+#epub_tocdup = True
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'http://docs.python.org/': None}
diff --git a/lecture_notes/source/index.rst b/lecture_notes/source/index.rst
new file mode 100644
index 0000000..b938b29
--- /dev/null
+++ b/lecture_notes/source/index.rst
@@ -0,0 +1,28 @@
+.. Software Engineering for Engineers and Scientists documentation master file, created by
+   sphinx-quickstart on Fri Jun 13 18:10:23 2014.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Software Engineering for Engineers and Scientists's documentation!
+=============================================================================
+
+Contents:
+
+.. toctree::
+   using_linux_tools/handout
+   basic_python/handout
+   advanced_python/handout
+   version_control/handout
+   latex/handout
+   test_driven_development/handout
+   :maxdepth: 2
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/lecture_notes/latex/handout.rst b/lecture_notes/source/latex/handout.rst
index 2177361..2177361 100644
--- a/lecture_notes/latex/handout.rst
+++ b/lecture_notes/source/latex/handout.rst
diff --git a/lecture_notes/latex/images/latex_not_wp.png b/lecture_notes/source/latex/images/latex_not_wp.png
index 1836d17..1836d17 100644
--- a/lecture_notes/latex/images/latex_not_wp.png
+++ b/lecture_notes/source/latex/images/latex_not_wp.png
diff --git a/lecture_notes/latex/index.rst b/lecture_notes/source/latex/index.rst
index cd0c36e..cd0c36e 100644
--- a/lecture_notes/latex/index.rst
+++ b/lecture_notes/source/latex/index.rst
diff --git a/lecture_notes/latex/lab_workbook.rst b/lecture_notes/source/latex/lab_workbook.rst
index 62eb78f..62eb78f 100644
--- a/lecture_notes/latex/lab_workbook.rst
+++ b/lecture_notes/source/latex/lab_workbook.rst
diff --git a/lecture_notes/latex/module_plan.rst b/lecture_notes/source/latex/module_plan.rst
index d30539a..d30539a 100644
--- a/lecture_notes/latex/module_plan.rst
+++ b/lecture_notes/source/latex/module_plan.rst
diff --git a/lecture_notes/test_driven_development/generate_testcases.py b/lecture_notes/source/test_driven_development/generate_testcases.py
index 17b48a7..17b48a7 100644
--- a/lecture_notes/test_driven_development/generate_testcases.py
+++ b/lecture_notes/source/test_driven_development/generate_testcases.py
diff --git a/lecture_notes/test_driven_development/lab_workbook.rst b/lecture_notes/source/test_driven_development/lab_workbook.rst
index fa5afa4..fa5afa4 100644
--- a/lecture_notes/test_driven_development/lab_workbook.rst
+++ b/lecture_notes/source/test_driven_development/lab_workbook.rst
diff --git a/lecture_notes/test_driven_development/math_utils/gcd.py b/lecture_notes/source/test_driven_development/math_utils/gcd.py
index 7204ac0..7204ac0 100644
--- a/lecture_notes/test_driven_development/math_utils/gcd.py
+++ b/lecture_notes/source/test_driven_development/math_utils/gcd.py
diff --git a/lecture_notes/test_driven_development/math_utils/gcd_testcases.dat b/lecture_notes/source/test_driven_development/math_utils/gcd_testcases.dat
index 3829b12..3829b12 100644
--- a/lecture_notes/test_driven_development/math_utils/gcd_testcases.dat
+++ b/lecture_notes/source/test_driven_development/math_utils/gcd_testcases.dat
diff --git a/lecture_notes/test_driven_development/math_utils/test_gcd.py b/lecture_notes/source/test_driven_development/math_utils/test_gcd.py
index c81c72b..c81c72b 100644
--- a/lecture_notes/test_driven_development/math_utils/test_gcd.py
+++ b/lecture_notes/source/test_driven_development/math_utils/test_gcd.py
diff --git a/lecture_notes/test_driven_development/tdd.rst b/lecture_notes/source/test_driven_development/tdd.rst
index 6347c47..6347c47 100644
--- a/lecture_notes/test_driven_development/tdd.rst
+++ b/lecture_notes/source/test_driven_development/tdd.rst
diff --git a/lecture_notes/using_linux_tools/examples/bar.txt b/lecture_notes/source/using_linux_tools/examples/bar.txt
index c0a5b08..c0a5b08 100644
--- a/lecture_notes/using_linux_tools/examples/bar.txt
+++ b/lecture_notes/source/using_linux_tools/examples/bar.txt
diff --git a/lecture_notes/using_linux_tools/examples/foo.txt b/lecture_notes/source/using_linux_tools/examples/foo.txt
index 1fe9426..1fe9426 100644
--- a/lecture_notes/using_linux_tools/examples/foo.txt
+++ b/lecture_notes/source/using_linux_tools/examples/foo.txt
diff --git a/lecture_notes/using_linux_tools/examples/items.txt b/lecture_notes/source/using_linux_tools/examples/items.txt
index e0828ee..e0828ee 100644
--- a/lecture_notes/using_linux_tools/examples/items.txt
+++ b/lecture_notes/source/using_linux_tools/examples/items.txt
diff --git a/lecture_notes/using_linux_tools/examples/marks.txt b/lecture_notes/source/using_linux_tools/examples/marks.txt
index f97b743..f97b743 100644
--- a/lecture_notes/using_linux_tools/examples/marks.txt
+++ b/lecture_notes/source/using_linux_tools/examples/marks.txt
diff --git a/lecture_notes/using_linux_tools/examples/marks1.txt b/lecture_notes/source/using_linux_tools/examples/marks1.txt
index 9a5299d..9a5299d 100644
--- a/lecture_notes/using_linux_tools/examples/marks1.txt
+++ b/lecture_notes/source/using_linux_tools/examples/marks1.txt
diff --git a/lecture_notes/using_linux_tools/examples/primes.txt b/lecture_notes/source/using_linux_tools/examples/primes.txt
index b5cdec8..b5cdec8 100644
--- a/lecture_notes/using_linux_tools/examples/primes.txt
+++ b/lecture_notes/source/using_linux_tools/examples/primes.txt
diff --git a/lecture_notes/using_linux_tools/examples/students.txt b/lecture_notes/source/using_linux_tools/examples/students.txt
index ddacd6b..ddacd6b 100644
--- a/lecture_notes/using_linux_tools/examples/students.txt
+++ b/lecture_notes/source/using_linux_tools/examples/students.txt
diff --git a/lecture_notes/using_linux_tools/examples/wonderland.txt b/lecture_notes/source/using_linux_tools/examples/wonderland.txt
index 0f62284..0f62284 100644
--- a/lecture_notes/using_linux_tools/examples/wonderland.txt
+++ b/lecture_notes/source/using_linux_tools/examples/wonderland.txt
diff --git a/lecture_notes/using_linux_tools/exercises.rst b/lecture_notes/source/using_linux_tools/exercises.rst
index 9898b39..9898b39 100644
--- a/lecture_notes/using_linux_tools/exercises.rst
+++ b/lecture_notes/source/using_linux_tools/exercises.rst
diff --git a/lecture_notes/using_linux_tools/handout.rst b/lecture_notes/source/using_linux_tools/handout.rst
index 5ef762a..5ef762a 100644
--- a/lecture_notes/using_linux_tools/handout.rst
+++ b/lecture_notes/source/using_linux_tools/handout.rst
diff --git a/lecture_notes/using_linux_tools/index.rst b/lecture_notes/source/using_linux_tools/index.rst
index beaf301..beaf301 100644
--- a/lecture_notes/using_linux_tools/index.rst
+++ b/lecture_notes/source/using_linux_tools/index.rst
diff --git a/lecture_notes/using_linux_tools/module_plan.rst b/lecture_notes/source/using_linux_tools/module_plan.rst
index 5557222..5557222 100644
--- a/lecture_notes/using_linux_tools/module_plan.rst
+++ b/lecture_notes/source/using_linux_tools/module_plan.rst
diff --git a/lecture_notes/version_control/exercises.rst b/lecture_notes/source/version_control/exercises.rst
index de55478..de55478 100644
--- a/lecture_notes/version_control/exercises.rst
+++ b/lecture_notes/source/version_control/exercises.rst
diff --git a/lecture_notes/version_control/handout.rst b/lecture_notes/source/version_control/handout.rst
index 6ee0317..6ee0317 100644
--- a/lecture_notes/version_control/handout.rst
+++ b/lecture_notes/source/version_control/handout.rst
diff --git a/lecture_notes/version_control/images/folder.png b/lecture_notes/source/version_control/images/folder.png
index 42d01a2..42d01a2 100644
--- a/lecture_notes/version_control/images/folder.png
+++ b/lecture_notes/source/version_control/images/folder.png
diff --git a/lecture_notes/version_control/images/mercurial_logo.png b/lecture_notes/source/version_control/images/mercurial_logo.png
index 4cd736e..4cd736e 100644
--- a/lecture_notes/version_control/images/mercurial_logo.png
+++ b/lecture_notes/source/version_control/images/mercurial_logo.png
diff --git a/lecture_notes/version_control/module_plan.rst b/lecture_notes/source/version_control/module_plan.rst
index 6ad7b47..6ad7b47 100644
--- a/lecture_notes/version_control/module_plan.rst
+++ b/lecture_notes/source/version_control/module_plan.rst