Release v0.4-alpha

Now with interface!

.gitignore

@@ -4,9 +4,6 @@
 # Word files
 *.docx
 
-# TeX files
-*.tex
-
 # TeX aux files
 *.aux
 

.travis.yml

@@ -1,23 +1,19 @@
-dist: trusty
-sudo: required
+dist: trusty  # 2014 Ubuntu, whoooo!
+sudo: required  # Necesary for installing LaTeX packages
 
-language: R
+language: python
+python: "3.5"
 
-install: true
+install: sudo apt-get update -qq  # No dependencies?
 
-script: true
+script: true  # No Testing
 
 
-after_success:
-    - sudo apt-get install texlive-latex-extra
-    - cd docs
-    - wget http://mirrors.ctan.org/macros/latex/contrib/standalone.zip
-    - unzip standalone.zip
-    - cd standalone
-    - wget http://texdoc.net/texmf-dist/tex/generic/ydoc/ydocstrip.tex
-    - xelatex standalone.ins
-    - cd .. && mv standalone/* .
-    - make travis && cd ..
+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
+    - make travis
+    - cd ..
 
 # Run tests on master & dev
 branches:
@@ -32,10 +28,11 @@ deploy:
     file: docs/persimmon.pdf
     skip_cleanup: true
     overwrite: true
+    prerelease: true
     on:
         branch:
             - master
 
-# Stop bothering me
 notifications:
-    email: false
+    email: false  # Stop bothering me
+

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2016 Álvaro Bermejo, Pedro García
+Copyright (c) 20177 Álvaro Bermejo
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/Makefile

@@ -1,69 +1,80 @@
 PDF := persimmon.pdf  # PDF Main Target
-MARKDOWN := introduction.md state_of_the_art.md objectives.md risk_analysis.md \
-	implementation.md postmortem.md  # Markdown files
+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..)
+#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
 
 GRAPHS := $(wildcard graphs/*.tex)  # Latex diagrams
-IMAGES := $(wildcard graphs/*.png)  # .png images
-IMAGES += $(GRAPHS:.tex=.pdf)  # Generated PDF Images
+IMAGES := $(wildcard images/*.png)  # .png images
+IMAGES += $(addprefix images/, $(notdir $(GRAPHS:.tex=.pdf)))  # Generated PDF Images
 
 all: $(PDF)
 
-# Main PDF, travis ci and book to print version
-$(PDF): $(BODY) $(TEMPLATE) $(IMAGES) # TODO: Add abstract
+
+$(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 scikitlearn 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) -o $@
+		--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 $@
 
-# Main PDF, travis ci and book to print version
 travis: $(BODY) $(APPENDIX) $(TEMPLATE) $(IMAGES)
 	pandoc --smart --standalone --latex-engine xelatex --template $(TEMPLATE) \
-		--metadata author:"Álvaro Bermejo" \
+		--metadata author:"Álvaro Bermejo" --metadata papersize:A4 \
 		--metadata date:"$(shell date +"%d/%m/%Y") ($(shell git describe --abbrev=0 --tags))" \
-		--metadata title:"Persimmon" --metadata fontsize:"12pt" --toc \
+		--metadata 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 colorlinks --metadata documentclass:"scrreprt" \
+		--metadata mainlang:English --metada keywords:"Machine Learning","Visual Programming" \
+		--metadata colorlinks --metadata documentclass:scrreprt \
 		--chapters $(BODY) $(APPENDIX) -o $(PDF)
 
-
-book_complu: $(BODY) $(APPENDIX) $(TEMPLATE) $(IMAGES)
+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 title:Persimmon --metadata fontsize:12pt --toc \
 		--metadata subtitle:"A scikitlearn visual programming interface" \
-		--metadata mainlang:"English" \
-		--metadata papersize:"A4" --metadata sansfont:"Helvetica Neue LT Com" \
-		--metadata documentclass:"scrbook" --metadata institute:"Universidad Complutense" \
-		--top-level-division chapter $(BODY) $(APPENDIX) -o bool_$(PDF)
+		--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
+	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)
 
-# For standalone images 
-graphs/%.pdf: graphs/%.tex
+# For standalone images
+images/%.pdf: graphs/%.tex
 	xelatex $< > /dev/null # TODO: actually output in graphs directory
-	mv $*.pdf graphs/
+	mv $*.pdf images/
 
 # Body and Appendices Middle Steps creation
-$(BODY): $(MARKDOWN)
+$(BODY): $(MARKDOWN) $(BIBLIOGRAPHY) $(CSL)
 	pandoc --no-tex-ligatures --bibliography $(BIBLIOGRAPHY) --csl $(CSL) \
 		metadata.yaml $(MARKDOWN) -o $@
 
 $(APPENDIX): $(APPENDICES)
 	pandoc --no-tex-ligatures $(APPENDICES) -o $@
 
 clean:
-	rm -f $(BODY) $(APPENDIX) graphs/*.pdf *.pdf *.log *.aux
+	rm -f $(BODY) $(APPENDIX) images/*.pdf *.pdf *.log *.aux
 
+test:
+	@echo $(GRAPHS)
+	@echo $(IMAGES)

docs/appendixX.md

@@ -8,14 +8,14 @@ Process
 -------
 Document is written on Pandoc's extended Markdown, and can be broken amongst
 different files. Images are inserted with regular Markdown syntax for images.
-A YAML file with metadata information is passed to pandoc, containing things 
+A YAML file with metadata information is passed to pandoc, containing things
 such as Author, Title, font, etc... The use of this information depends on
 what output we are creating and the template/reference we are using.
 
 
 Diagrams
 --------
-Diagrams are were created with LaTeX packages such as tikz or pgfgantt, they 
+Diagrams are were created with LaTeX packages such as tikz or pgfgantt, they
 can be inserted directly as PDF, but if we desire to output to formats other
 than LaTeX is more convenient to convert them to .png filesi with tools such
 as `pdftoppm`.

docs/graphs/regular_workflow.tex

@@ -0,0 +1,22 @@
+\documentclass{standalone}
+
+\usepackage{tikz}
+
+\begin{document}
+  \begin{tikzpicture}
+    \draw (-0.5, -2.3) rectangle (0.5, -1) node[midway, gray] {.csv};
+    \draw [->, gray, thick] (0, -0.9) -- (0, -0.4);
+    \draw (0, 0) ellipse (28pt and 10pt) node {Estimator};
+    \draw [->, gray, thick] (1.1, 0) -- (1.9, 0);
+    \draw (3, 0) ellipse (28pt and 10pt) node {Adjustment};
+    \draw [->, gray, thick] (4.1, 0) -- (4.9, 0);
+    \draw (6, 0) ellipse (28pt and 10pt) node {Validation};
+    \draw [->, gray, thick] (7.1, 0) -- (7.9, 0);
+    \draw (9, 0) ellipse (28pt and 10pt) node {Prediction};
+    \draw [->, gray, thick] (9, -0.9) -- (9, -0.4);
+    \draw (8.5, -2.3) rectangle (9.5, -1) node[midway, gray] {.csv};
+    \draw [->, gray, thick] (10.1, 0) --(10.9, 0);
+    \draw (11, -0.65) rectangle (12, 0.65) node[midway, gray] {.csv};
+  \end{tikzpicture}
+\end{document}
+

docs/graphs/simpler_workflow.tex

@@ -0,0 +1,20 @@
+\documentclass{standalone}
+
+\usepackage{tikz}
+
+\begin{document}
+  \begin{tikzpicture}
+    \draw (-0.5, -2.3) rectangle (0.5, -1) node[midway, gray] {.csv};
+    \draw [->, gray, thick] (0, -0.9) -- (0, -0.4);
+    \draw (0, 0) ellipse (28pt and 10pt) node {Estimator};
+    \draw [->, gray, thick] (1.1, 0) -- (1.9, 0);
+    \draw (3, 0) ellipse (28pt and 10pt) node {Validation};
+    \draw [->, gray, thick] (4.1, 0) -- (4.9, 0);
+    \draw (6, 0) ellipse (28pt and 10pt) node {Prediction};
+    \draw [->, gray, thick] (6, -0.9) -- (6, -0.4);
+    \draw (5.5, -2.3) rectangle (6.5, -1) node[midway, gray] {.csv};
+    \draw [->, gray, thick] (7.1, 0) --(7.9, 0);
+    \draw (8, -0.65) rectangle (9, 0.65) node[midway, gray] {.csv};
+  \end{tikzpicture}
+\end{document}
+

docs/graphs/simplest_workflow.tex

@@ -0,0 +1,16 @@
+\documentclass{standalone}
+
+\usepackage{tikz}
+
+\begin{document}
+  \begin{tikzpicture}
+    \draw (-0.5, -2.3) rectangle (0.5, -1) node[midway, gray] {.csv};
+    \draw [->, gray, thick] (0, -0.9) -- (0, -0.4);
+    \draw (0, 0) ellipse (28pt and 10pt) node {Estimator};
+    \draw [->, gray, thick] (1.1, 0) -- (1.9, 0);
+    \draw (3, 0) ellipse (28pt and 10pt) node {Validation};
+    %\draw [->, gray, thick] (4.1, 0) -- (4.9, 0);
+    %\draw (6, 0) ellipse (28pt and 10pt) node {Prediction};
+  \end{tikzpicture}
+\end{document}
+

docs/implementation.md

@@ -3,9 +3,14 @@ Implementation
 
 First Iteration
 ---------------
+For the first iteration the priority was to get a proof of concept in order to
+see where the difficulties can appear, a few simple classificators and
+cross-validation techniques.
 
-![Early "static" interface](graphs/early_interface.png)
-
-![File chooser](graphs/filechooser.png)
+![Button based first interface](images/interface5.png)
 
+Second Iteration
+----------------
 
+Third Iteration
+---------------