Release v0.5-beta

First beta release!

Code
* Real interface now implemented
* Blocks can be dragged, connected, reconnected and executed
* The whole blackboard can be moved and zoomed

Documentation
* Expanded sections
* Added appendix
* Added algorithms graphs

Author: AlvarBer

.gitignore

@@ -6,10 +6,25 @@
 
 # TeX aux files
 *.aux
+*.log
+*.tex
+
+# Except graphs
+!docs/graphs/*.tex
 
 # Vim Backup files
 *.swp
 *~
 
 # Python cache folders
-__pycache__
+__pycache__/
+
+# PyInstaller folders
+build/
+dist/
+
+# Egg info
+*.egg-info/
+
+# CSV Files
+*.csv

.travis.yml

@@ -11,7 +11,7 @@ script: true  # No Testing
 
 after_success:  # Build binaries and documentation
     - cd docs  # Time to do documentation
-    - sudo apt-get install -y --no-install-recommends pandoc pandoc-citeproc texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra texlive-xetex lmodern pgf
+    - sudo apt-get install -y --no-install-recommends pandoc pandoc-citeproc texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra texlive-xetex lmodern pgf texlive-science
     - make travis
     - cd ..
 

docs/Makefile

@@ -1,80 +1,104 @@
 PDF := persimmon.pdf  # PDF Main Target
-MARKDOWN := introduction.md state_of_the_art.md workflow.md objectives.md \
-	risk_analysis.md implementation.md postmortem.md  # Markdown files
-BODY := body.tex  # Markdown files will be converted to this intermediate step
-#APPENDICES := appendixX.md  # Markdown Appendices
-#APPENDIX := appendix.tex  # And appendices to this intermediate step
-#METADATA := metadata.yaml  # Metadata files (Author, Date, Title, etc..)
+MARKDOWN := introduction.md state_of_the_art.md workflow.md milestones.md \
+	risk_analysis.md interface.md implementation.md type_checking.md \
+	postmortem.md  # Markdown files
+MARKDOWN_COMPLUTENSE := introduction.md focus.md state_of_the_art.md \
+	workflow.md milestones.md risk_analysis.md interface.md implementation.md \
+	type_checking.md postmortem.md
+APPENDICES := appendixA.md appendixB.md  # Appendix after bibliography
+METADATA := metadata.yaml  # Metadata files (Author, Date, Title, etc..)
 BIBLIOGRAPHY := persimmon.bib  # BibLaTeX bibliography
 CSL := emerald-harvard.csl  # CSL file used for citations
 TEMPLATE := template.tex  # LaTeX template for producing PDF
 
+# Add src prefix to markdown files
+MARKDOWN := $(addprefix src/, $(MARKDOWN))
+MARKDOWN_COMPLUTENSE := $(addprefix src/, $(MARKDOWN_COMPLUTENSE))
+APPENDICES := $(addprefix src/, $(APPENDICES))
+
 GRAPHS := $(wildcard graphs/*.tex)  # Latex diagrams
 IMAGES := $(wildcard images/*.png)  # .png images
-IMAGES += $(addprefix images/, $(notdir $(GRAPHS:.tex=.pdf)))  # Generated PDF Images
+# Generated PDF Images
+IMAGES += $(addprefix images/, $(notdir $(GRAPHS:.tex=.pdf)))
 
-all: $(PDF)
+# Intermediate tex files required for appending after bibliography
+BODY := body.tex
+APPENDIX := appendices.tex
+BODY_COMPLUTENSE := body_complutense.tex
 
+all: $(PDF)
 
-$(PDF): $(BODY) $(APPENDIX) $(TEMPLATE) $(IMAGES) # TODO: Add abstract
-	pandoc --smart --standalone --latex-engine xelatex --template $(TEMPLATE) \
-		--metadata author:"Álvaro Bermejo" \
-		--metadata date:"$(shell date +"%d/%m/%Y") ($(shell git describe --abbrev=0 --tags))" \
-		--metadata title:Persimmon --metadata fontsize:12pt --toc \
-		--metadata subtitle:"A sklearn visual programming interface" \
-		--metadata mainlang:English --metada keywords:"Machine Learning","Visual Programming" \
-		--metadata papersize:A4 --metadata sansfont:"Helvetica Neue LT Com" \
-		--metadata colorlinks --metadata documentclass:scrreprt \
-		--top-level-division chapter $(BODY) $(APPENDIX) -o $@
-
-travis: $(BODY) $(APPENDIX) $(TEMPLATE) $(IMAGES)
+$(PDF): $(BODY) $(APPENDIX) $(TEMPLATE) $(IMAGES)
 	pandoc --smart --standalone --latex-engine xelatex --template $(TEMPLATE) \
-		--metadata author:"Álvaro Bermejo" --metadata papersize:A4 \
-		--metadata date:"$(shell date +"%d/%m/%Y") ($(shell git describe --abbrev=0 --tags))" \
-		--metadata title:Persimmon --metadata fontsize:12pt --toc \
-		--metadata subtitle:"A sklearn visual programming interface" \
-		--metadata mainlang:English --metada keywords:"Machine Learning","Visual Programming" \
-		--metadata colorlinks --metadata documentclass:scrreprt \
-		--chapters $(BODY) $(APPENDIX) -o $(PDF)
-
-complutense: $(BODY) $(APPENDIX) $(TEMPLATE) $(IMAGES)
-	pandoc --smart --standalone --latex-engine xelatex --template $(TEMPLATE) \
-		--metadata author:"Álvaro Bermejo" --metadata date:"Director: Pablo Moreno Ger" \
-		--metadata title:Persimmon --metadata fontsize:12pt --toc \
-		--metadata subtitle:"A scikitlearn visual programming interface" \
-		--metadata mainlang:English --metadata colorlinks --metadata titlepic:images/fdi.png \
-		--metadata papersize:A4 --metadata sansfont:"Helvetica Neue LT Com" \
-		--metadata documentclass:scrreprt --metadata institute:"Universidad Complutense" \
-		--metada keywords:"Machine Learning","Visual Programming","Serious Games" \
-		--top-level-division chapter $(BODY) $(APPENDIX) -o $(PDF)
-
-twocol: $(BODY) $(APPENDIX) $(TEMPLATE) $(IMAGES)  # Adjust Spacing with geometry
+		--table-of-contents --top-level-division chapter \
+		--metadata author:"Álvaro Bermejo García" --metadata title:Persimmon \
+		--metadata subtitle:"A visual programming interface for machine learning" \
+		--metadata date:"$(shell date +%Y/%m/%d)" --metadata documentclass:scrreprt \
+		--metadata sansfont:"Helvetica Neue LT Com" --metadata colorlinks \
+		--metadata lof --metadata papersize:A4 --metadata fontsize:12pt \
+		--metadata mainlang:English \
+		--metadata keywords:"Dataflow Programming","Machine Learning","Visual Programming","Compilers" \
+		--metadata abstract:"Persimmon is a visual programming interface that leverages scikit-learn to provide\
+		a drag and drop interface for creating Machine Learning pipelines." \
+		$(BODY) $(APPENDIX) -o $@
+
+
+complutense: $(BODY_COMPLUTENSE) $(APPENDIX) $(TEMPLATE) $(IMAGES)
 	pandoc --smart --standalone --latex-engine xelatex --template $(TEMPLATE) \
-		--metadata author:"Álvaro Bermejo" --metadata colorlinks \
-		--metadata date:"$(shell date +"%d/%m/%Y") ($(shell git describe --abbrev=0 --tags))" \
-		--metadata title:Persimmon --metadata fontsize:12p --toc \
-		--metadata subtitle:"A sklearn visual programming interface" \
-		--metadata mainlang:English --metada keywords:"Machine Learning","Visual Programming" \
-		--metadata papersize:A4 --metadata classoption:twocolumn \
-		--metadata sansfont:"Helvetica Neue LT Com" --metadata documentclass:scrreprt \
-		--top-level-division chapter $(BODY) $(APPENDIX) -o $(PDF)
+		--table-of-contents --top-level-division chapter \
+		--metadata author:"Álvaro Bermejo García" \
+		--metadata title:"A scikit-learn visual programming interface" \
+		--metadata date:"Director:Manuel Freire Moran, Codirector: Pablo Moreno Ger" \
+		--metadata documentclass:scrreprt \
+		--metadata sansfont:"Helvetica Neue LT Com" --metadata colorlinks \
+		--metadata lof --metadata papersize:A4 --metadata fontsize:12pt \
+		--metadata mainlang:English \
+		--metadata keywords:"Serious Learning","Machine Learning","Visual Programming" \
+		--metadata titlepic:images/fdi.png $(BODY_COMPLUTENSE) $(APPENDIX) \
+		-o $(PDF)
+
 
 # For standalone images
 images/%.pdf: graphs/%.tex
-	xelatex $< > /dev/null # TODO: actually output in graphs directory
+	xelatex $< > /dev/null
 	mv $*.pdf images/
+	rm -f $*.log $*.aux
 
-# Body and Appendices Middle Steps creation
 $(BODY): $(MARKDOWN) $(BIBLIOGRAPHY) $(CSL)
-	pandoc --no-tex-ligatures --bibliography $(BIBLIOGRAPHY) --csl $(CSL) \
-		metadata.yaml $(MARKDOWN) -o $@
+	pandoc --no-tex-ligatures --top-level-division chapter \
+		--bibliography $(BIBLIOGRAPHY) --csl $(CSL) $(MARKDOWN) -o $@
+
+
+$(BODY_COMPLUTENSE): $(MARKDOWN_COMPLUTENSE) $(BIBLIOGRAPHY) $(CSL)
+	pandoc --no-tex-ligatures --top-level-division chapter --table -of-contents \
+		--bibliography $(BIBLIOGRAPHY) --csl $(CSL) $(MARKDOWN_COMPLUTENSE) \
+		-o $@
 
 $(APPENDIX): $(APPENDICES)
-	pandoc --no-tex-ligatures $(APPENDICES) -o $@
+	pandoc --no-tex-ligatures --top-level-division chapter $(APPENDICES) -o $@
+
+# Travis generation, only necessary because travis version of pandoc is old.
+BODY_TRAVIS := body_travis.tex
+
+travis: $(BODY_TRAVIS) $(APPENDIX_TRAVIS) $(TEMPLATE) $(IMAGES)
+	pandoc --smart --standalone --latex-engine xelatex --template $(TEMPLATE) \
+		--table-of-contents --chapters \
+		--metadata author:"Álvaro Bermejo García" --metadata title:Persimmon \
+		--metadata subtitle:"A scikit-learn visual programming interface" \
+		--metadata date:2017-02-18 --metadata documentclass:scrreprt \
+		--metadata colorlinks --metadata lof --metadata papersize:A4 \
+		--metadata fontsize:12pt --metadata mainlang:English \
+		--metadata keywords:"Machine Learning","Visual Programming" \
+		$(BODY_TRAVIS) $(APPENDIX_TRAVIS) -o $(PDF)
+
+$(BODY_TRAVIS): $(MARKDOWN) $(BIBLIOGRAPHY) $(CSL)
+	pandoc --no-tex-ligatures --chapters --bibliography $(BIBLIOGRAPHY) --csl \
+		$(CSL) $(MARKDOWN) -o $@
+
+$(APPENDIX_TRAVIS): $(APPENDICES)
+	pandoc --no-tex-ligatures --chapters $(APPENDICES) -o $@
+
 
 clean:
-	rm -f $(BODY) $(APPENDIX) images/*.pdf *.pdf *.log *.aux
+	rm -f images/*.pdf $(PDF) *.log *.aux $(BODY) $(APPENDIX)
 
-test:
-	@echo $(GRAPHS)
-	@echo $(IMAGES)

docs/graphs/graph_execution.tex

@@ -0,0 +1,37 @@
+\documentclass[12pt, varwidth=20cm]{standalone}
+
+\usepackage[noend]{algpseudocode}
+
+\begin{document}
+  \begin{algorithmic}[1]
+    \Require G is a Directed Acyclic Graph that does not break
+    type safety on all the relationships.
+    \Function{execute}{$G: Graph$}
+      \State $queue \gets Queue()$
+      \State $seen \gets Map()$
+      \State $queue.put(G.get\_input\_blocks())$ \Comment {We can start in a random vertex}
+      \While {$\neg queue.empty()$}
+        \State $queue$, $seen \gets$ \Call {explore}{queue.get(), queue, seen}
+      \EndWhile
+    \EndFunction
+    \\
+    \Function{explore}{$current: Vertex,$ $queue: Queue, seen: Map$}{ $\to$ $Queue,$ $Map$}
+      \ForAll {$in\_pin \in current.get\_in\_pins()$}
+        \State $corresponding \gets in\_pin.origin.uid$
+        \If {$\neg seen.has(corresponding)$}
+          \State $dependency \gets corresponding.block$
+          \If {$dependency \in queue$} \Comment {Remove if already in queue}
+            \State $queue.remove(dependency)$
+          \EndIf
+          \State $queue$, $seen \gets$ \Call {explore}{dependency, queue, seen}
+        \EndIf
+        \State $in\_pin.value \gets seen.get(corresponding)$
+      \EndFor
+      \State $current.function()$ \Comment {function uses in\_pins and sets out\_pins}
+      \ForAll {$out\_pin \in current.get\_out\_pins()$}
+        \State $seen.put(out\_pin, out\_pin.value)$
+      \EndFor
+      \State \Return $queue$, $seen$
+    \EndFunction
+  \end{algorithmic}
+\end{document}

docs/graphs/packages.tex

@@ -0,0 +1,15 @@
+\documentclass{standalone}
+
+\usepackage{tikz}
+
+\begin{document}
+  \begin{tikzpicture}[sibling distance=10em,
+    every node/.style = {shape=rectangle,
+      draw, align=center}]
+  \node {persimmon}
+    child { node {backend} }
+    child { node {view}
+      child { node {blocks} }
+      child { node {util} } };
+\end{tikzpicture}
+\end{document}