* Added Makefile

* Package docs are now generated from Makefile

Makefile

@@ -0,0 +1,45 @@
+DOCS=docs
+DOCS_IMAGES_RAW=$(DOCS)/images
+DOCS_IMAGES_ANNOTATED=$(DOCS_IMAGES_RAW)/annotated
+ANNOTATED_TIKZ=$(wildcard $(DOCS_IMAGES_ANNOTATED)/*.tikz)
+ANNOTATED_JPGS=$(patsubst %.tikz, %.jpg, $(ANNOTATED_TIKZ))
+PKG_DOCS=optoConfig96/resources/docs
+
+all: generate_package
+
+generate_docs: $(ANNOTATED_JPGS) $(DOCS)/optoConfig96_guide.html README.md
+
+$(DOCS_IMAGES_ANNOTATED)/%.jpg: $(DOCS_IMAGES_ANNOTATED)/%.tikz
+	cd $(DOCS_IMAGES_ANNOTATED) ; \
+		pdflatex  $(notdir $<)
+	gs -sDEVICE=png16m -dJPEGQ=90 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 \
+		-dDOINTERPOLATE -r95 -o $@ $(patsubst %.tikz, %.pdf, $<)
+	rm $(DOCS_IMAGES_ANNOTATED)/*.{aux,log,pdf}
+
+$(DOCS)/optoConfig96_guide.html: $(DOCS)/guide.md
+	pandoc -s $< --css guide.css -o $@
+
+README.md: $(DOCS)/guide.md
+	# Ignore YAML header
+	tail -n+5 docs/guide.md > README.md
+	# Make image paths relative to root
+	sed -i "s|images/|docs/images/|g" README.md
+
+generate_package: generate_docs
+	# Copy docs to resources folder to make the documentation available from
+	# within the application
+	rm -rf $(PKG_DOCS)
+	mkdir -p $(PKG_DOCS)/images/annotated
+	cp $(DOCS)/*.{css,html} $(PKG_DOCS)
+	cp $(DOCS)/images/*.jpg $(PKG_DOCS)/images
+	cp $(DOCS)/images/annotated/*.jpg $(PKG_DOCS)/images/annotated
+	python -m build
+
+.PHONY: test_install
+test_install:
+	rm -rf test_install
+	mkdir test_install ; cd test_install ; \
+		python -m venv test_install_venv ; \
+		source test_install_venv/bin/activate ; \
+		pip install ../dist/optoConfig96-1.0.3.tar.gz ; \
+		python -m optoConfig96

docs/images/annotated/annotation_template.tex → docs/images/annotated/annotation_preamble.tex

@@ -1,5 +1,5 @@
 \documentclass{article}
-\usepackage[paperwidth=1920px, paperheight=1080px, textwidth=1920px , textheight=1080px, margin=0pt]{geometry}
+\usepackage[margin=0pt]{geometry}
 \usepackage[utf8]{inputenc}
 \usepackage[T1]{fontenc}
 \usepackage{sans} % font
@@ -9,14 +9,9 @@
 \usepackage[active, tightpage]{preview}
 \PreviewEnvironment[]{tikzpicture}
 \usetikzlibrary{shapes, arrows.meta, calc, intersections, decorations.text, positioning}
-\graphicspath{{/home/oliver/Code/optoPlate96/python/docs/images/}}
 
 \tikzset{
     every node/.append style={inner sep=5pt, outer sep=0},
     imgnode/.style={inner sep=0, outer sep=0, anchor=south west, align=center},
     number/.append style={draw=red!50, line width=2pt, fill=red!10, circle, font=\fontsize{70pt}{70pt}\bfseries\selectfont}
 }
-
-\begin{document}
-<>
-\end{document}

docs/images/annotated/bulk_assign.tikz

@@ -1,14 +1,17 @@
-\begin{tikzpicture}[>=stealth, line width=3pt]
+\input{annotation_preamble}
+\PassOptionsToPackage{paperwidth=1920px, paperheight=1080px, textwidth=1920px, textheight=1080px}{geometry}
 
+\begin{document}
+\begin{tikzpicture}[>=stealth, line width=3pt]
 \tikzset{
 		line/.style={
 				draw, white, line width=8pt, ->,
 				postaction={draw, red, line width=3pt, shorten >=6pt}
 		}
 }
 
-\node (image) [imgnode] {\includegraphics{bulk_assign_programs}};
-\node (image2) [imgnode, below=2cm of image] {\includegraphics{bulk_assign_wells}};
+\node (image) [imgnode] {\includegraphics{../bulk_assign_programs}};
+\node (image2) [imgnode, below=2cm of image] {\includegraphics{../bulk_assign_wells}};
 
 \draw[->, >=stealth] (image) -- (image2) node[midway, right] {\resizebox{3.5cm}{!}{Bulk assign}};
 
@@ -22,3 +25,4 @@
 \end{scope}
 
 \end{tikzpicture}
+\end{document}

docs/images/annotated/overview.tikz

@@ -1,8 +1,8 @@
-\begin{tikzpicture}%[remember picture, overlay]
-%\begin{scope}[shift={(current page.south west)}]
-
-
+\input{annotation_preamble}
+\PassOptionsToPackage{paperwidth=1920px, paperheight=1080px, textwidth=1920px, textheight=1080px}{geometry}
 
+\begin{document}
+\begin{tikzpicture}
 \node (image) [imgnode,draw] {\includegraphics{overview}};
 
 
@@ -16,5 +16,5 @@
 \node[number] at (0.25, 0.25) {5};
 \node[number] at (0.75, 0.25) {6};
 \end{scope}
-
 \end{tikzpicture}
+\end{document}

docs/optoConfig96_guide.html

@@ -24,7 +24,7 @@
 <h1 class="title">optoConfig-96 User Guide</h1>
 </header>
 <h1 id="optoconfig-96---interactive-configuration-of-experiments-using-the-optoplate-96">optoConfig-96 - Interactive configuration of experiments using the optoPlate-96</h1>
-<p>User guide for version 1.0.2.</p>
+<p>User guide for version 1.0.3.</p>
 <p>If optoConfig-96 was useful to you, please consider citing the paper:</p>
 <p>Thomas, OS, Hörner, M &amp; Weber, W: A graphical user interface to design high-throughput optogenetic experiments with the optoPlate-96. <em>Nat Protoc</em> (2020). https://doi.org/10.1038/s41596-020-0349-x</p>
 <h1 id="installation-instructions">Installation Instructions</h1>
@@ -60,7 +60,7 @@ <h2 id="as-a-python-package">As a Python package</h2>
 <ol type="1">
 <li><p>Clone the repository by entering:</p>
 <p><code>git clone https://github.com/WeberSynBioLab/optoConfig-96.git</code></p>
-<p>in a terminal. Alternatively, download the package from the <a href="https://github.com/WeberSynBioLab/optoConfig-96/releases">GitHub <em>Releases</em> page</a>. The package is not yet on <a href="https://www.pypi.org">PyPI</a>.</p>
+<p>in a terminal. Alternatively, download the package from the <a href="https://github.com/WeberSynBioLab/optoConfig-96/releases">GitHub <em>Releases</em> page</a>.</p>
 <ol type="1">
 <li>If you cloned the repository, you will first have to prepare the package by running <code>python setup.py build sdist</code> in a terminal, in the directory in which the optoConfig-96 <code>setup.py</code> is located.</li>
 <li>The package will be created at <code>dist/optoConfig96-x.x.x.tar.gz</code>, where <code>x.x.x</code> denotes the current version.</li>

optoConfig96/resources/docs/optoConfig96_guide.html

@@ -24,7 +24,7 @@
 <h1 class="title">optoConfig-96 User Guide</h1>
 </header>
 <h1 id="optoconfig-96---interactive-configuration-of-experiments-using-the-optoplate-96">optoConfig-96 - Interactive configuration of experiments using the optoPlate-96</h1>
-<p>User guide for version 1.0.2.</p>
+<p>User guide for version 1.0.3.</p>
 <p>If optoConfig-96 was useful to you, please consider citing the paper:</p>
 <p>Thomas, OS, Hörner, M &amp; Weber, W: A graphical user interface to design high-throughput optogenetic experiments with the optoPlate-96. <em>Nat Protoc</em> (2020). https://doi.org/10.1038/s41596-020-0349-x</p>
 <h1 id="installation-instructions">Installation Instructions</h1>
@@ -60,7 +60,7 @@ <h2 id="as-a-python-package">As a Python package</h2>
 <ol type="1">
 <li><p>Clone the repository by entering:</p>
 <p><code>git clone https://github.com/WeberSynBioLab/optoConfig-96.git</code></p>
-<p>in a terminal. Alternatively, download the package from the <a href="https://github.com/WeberSynBioLab/optoConfig-96/releases">GitHub <em>Releases</em> page</a>. The package is not yet on <a href="https://www.pypi.org">PyPI</a>.</p>
+<p>in a terminal. Alternatively, download the package from the <a href="https://github.com/WeberSynBioLab/optoConfig-96/releases">GitHub <em>Releases</em> page</a>.</p>
 <ol type="1">
 <li>If you cloned the repository, you will first have to prepare the package by running <code>python setup.py build sdist</code> in a terminal, in the directory in which the optoConfig-96 <code>setup.py</code> is located.</li>
 <li>The package will be created at <code>dist/optoConfig96-x.x.x.tar.gz</code>, where <code>x.x.x</code> denotes the current version.</li>