Updates to project structure pt 1

.gitignore

@@ -1,3 +1,6 @@
 __pycache__/
 env/
 output/
+build/*.md
+build/*.tex
+build/*.html

Makefile

@@ -4,6 +4,7 @@ PELICANOPTS=
 
 BASEDIR=$(CURDIR)
 INPUTDIR=$(BASEDIR)/content
+BUILDDIR=$(BASEDIR)/build
 OUTPUTDIR=$(BASEDIR)/output
 CONFFILE=$(BASEDIR)/pelicanconf.py
 PUBLISHCONF=$(BASEDIR)/publishconf.py
@@ -64,15 +65,15 @@ help:
 
 html:
 	./convert.py html
-	$(PELICAN) $(INPUTDIR) -o $(OUTPUTDIR) -s $(CONFFILE) $(PELICANOPTS)
+	$(PELICAN) $(BUILDDIR) -o $(OUTPUTDIR) -s $(CONFFILE) $(PELICANOPTS)
 
 pdf:
 	./convert.py tex
-	cd $(INPUTDIR); rubber thesis
+	cd $(BUILDDIR); rubber thesis
 
 clean:
 	[ ! -d $(OUTPUTDIR) ] || rm -rf $(OUTPUTDIR)
-	cd $(INPUTDIR); rubber --clean thesis; rm -f *_*.tex; rm -f *_*.html; rm -f *_*.aux
+	cd $(BUILDDIR); rubber --clean thesis; rm -f *_*.tex; rm -f *_*.html; rm -f *_*.aux
 
 regenerate:
 	$(PELICAN) -r $(INPUTDIR) -o $(OUTPUTDIR) -s $(CONFFILE) $(PELICANOPTS)
@@ -104,8 +105,8 @@ stopserver:
 	@echo 'Stopped Pelican and SimpleHTTPServer processes running in background.'
 
 publish:
-	$(PELICAN) $(INPUTDIR) -o $(OUTPUTDIR) -s $(PUBLISHCONF) $(PELICANOPTS)
-	[ -f content/thesis.pdf ] && cp $(INPUTDIR)/thesis.pdf $(OUTPUTDIR)
+	$(PELICAN) $(BUILDDIR) -o $(OUTPUTDIR) -s $(PUBLISHCONF) $(PELICANOPTS)
+	[ -f content/thesis.pdf ] && cp $(BUILDDIR)/thesis.pdf $(OUTPUTDIR)
 
 ssh_upload: publish
 	scp -P $(SSH_PORT) -r $(OUTPUTDIR)/* $(SSH_USER)@$(SSH_HOST):$(SSH_TARGET_DIR)

content/american-physics-society.csl

@@ -1,157 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
-  <info>
-    <title>American Physics Society</title>
-    <title-short>APS</title-short>
-    <id>http://www.zotero.org/styles/american-physics-society</id>
-    <link href="http://www.zotero.org/styles/american-physics-society" rel="self"/>
-    <link href="http://www.zotero.org/styles/american-institute-of-physics" rel="template"/>
-    <link href="http://authors.aps.org/STYLE/ms.html#citations" rel="documentation"/>
-    <author>
-      <name>Richard Karnesky</name>
-      <email>karnesky+zotero@gmail.com</email>
-      <uri>http://arc.nucapt.northwestern.edu/Richard_Karnesky</uri>
-    </author>
-    <category citation-format="numeric"/>
-    <category field="physics"/>
-    <summary>Common style use by APS publications.</summary>
-    <updated>2015-01-21T22:37:41+00:00</updated>
-    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
-  </info>
-  <macro name="author">
-    <names variable="author">
-      <name delimiter=", " initialize-with=". " and="text"/>
-      <label form="long" prefix=", " suffix=" "/>
-      <substitute>
-        <names variable="editor"/>
-        <names variable="translator"/>
-      </substitute>
-    </names>
-  </macro>
-  <macro name="editor">
-    <names variable="editor">
-      <label form="verb" suffix=" "/>
-      <name delimiter=", " initialize-with=". " and="text"/>
-    </names>
-  </macro>
-  <macro name="year-date">
-    <choose>
-      <if variable="issued">
-        <date variable="issued">
-          <date-part name="year"/>
-        </date>
-      </if>
-      <else>
-        <text term="no date" form="short"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="day-date">
-    <choose>
-      <if variable="issued">
-        <date variable="issued">
-          <date-part name="day" suffix=" "/>
-          <date-part name="month" form="long" suffix=" "/>
-          <date-part name="year"/>
-        </date>
-      </if>
-      <else>
-        <text term="no date" form="short"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="publisher">
-    <group prefix="(" suffix=")" delimiter=", ">
-      <text variable="publisher"/>
-      <text variable="publisher-place" text-case="title"/>
-      <text macro="year-date"/>
-    </group>
-  </macro>
-  <macro name="edition">
-    <choose>
-      <if is-numeric="edition">
-        <group delimiter=" ">
-          <number variable="edition" form="ordinal"/>
-          <text term="edition" form="short"/>
-        </group>
-      </if>
-      <else>
-        <text variable="edition"/>
-      </else>
-    </choose>
-  </macro>
-  <citation collapse="citation-number">
-    <sort>
-      <key variable="citation-number"/>
-    </sort>
-    <layout delimiter="," prefix="&#160;[" suffix="]">
-      <text variable="citation-number"/>
-    </layout>
-  </citation>
-  <bibliography entry-spacing="0" second-field-align="flush">
-    <layout suffix=".">
-      <text variable="citation-number" prefix="[" suffix="]"/>
-      <text macro="author" suffix=", "/>
-      <choose>
-        <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-          <group delimiter=" ">
-            <group delimiter=", ">
-              <text variable="title" text-case="title" font-style="italic"/>
-              <text macro="edition"/>
-            </group>
-            <group delimiter=", ">
-              <text macro="publisher"/>
-              <group delimiter=" ">
-                <label variable="page" form="short"/>
-                <text variable="page"/>
-              </group>
-            </group>
-          </group>
-        </if>
-        <else-if type="chapter paper-conference" match="any">
-          <group delimiter=" ">
-            <text term="in"/>
-            <group delimiter=", ">
-              <text variable="container-title" form="short" text-case="title" font-style="italic"/>
-              <text macro="editor"/>
-              <text macro="edition"/>
-            </group>
-            <group delimiter=", ">
-              <text macro="publisher"/>
-              <group delimiter=" ">
-                <label variable="page" form="short"/>
-                <text variable="page"/>
-              </group>
-            </group>
-          </group>
-        </else-if>
-        <else-if type="patent">
-          <group delimiter=" ">
-            <text variable="number"/>
-            <text macro="day-date" prefix="(" suffix=")"/>
-          </group>
-        </else-if>
-        <else-if type="thesis">
-          <group delimiter=", ">
-            <text variable="title" text-case="title"/>
-            <text variable="genre"/>
-            <text variable="publisher"/>
-            <text macro="year-date"/>
-          </group>
-        </else-if>
-        <else>
-          <group delimiter=" ">
-            <text variable="container-title" form="short" text-case="title"/>
-            <group delimiter=", ">
-              <text variable="volume" font-weight="bold"/>
-              <group delimiter=" ">
-                <text variable="page-first" form="short"/>
-                <text macro="year-date" prefix="(" suffix=")"/>
-              </group>
-            </group>
-          </group>
-        </else>
-      </choose>
-    </layout>
-  </bibliography>
-</style>

content/chapter.html

@@ -1,12 +0,0 @@
-<html>
-    <head>
-        <title>$title$</title>
-        $if(modified)$
-        <meta name="modified" content="$modified$" />
-        <meta name="category" content="thesis" />
-        $endif$
-    </head>
-    <body>
-$body$
-    </body>
-</html>

content/chapter.latex

@@ -1,4 +0,0 @@
-\chapter{$title$}
-
-$body$
-

content/figures/fr_schem.svg

@@ -0,0 +1,303 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   width="190.09734mm"
+   height="171.94856mm"
+   viewBox="0 0 190.09734 171.94856"
+   version="1.1"
+   id="svg8"
+   inkscape:export-filename="/home/caleb/fr3.png"
+   inkscape:export-xdpi="157.554"
+   inkscape:export-ydpi="157.554"
+   inkscape:version="0.92.2 2405546, 2018-03-11"
+   sodipodi:docname="fr_schem.svg">
+  <defs
+     id="defs2" />
+  <sodipodi:namedview
+     id="base"
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1.0"
+     inkscape:pageopacity="0.0"
+     inkscape:pageshadow="2"
+     inkscape:zoom="1.4"
+     inkscape:cx="342.30069"
+     inkscape:cy="309.55685"
+     inkscape:document-units="mm"
+     inkscape:current-layer="layer1"
+     showgrid="false"
+     inkscape:window-width="2526"
+     inkscape:window-height="1556"
+     inkscape:window-x="357"
+     inkscape:window-y="408"
+     inkscape:window-maximized="0" />
+  <metadata
+     id="metadata5">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+        <dc:title></dc:title>
+      </cc:Work>
+    </rdf:RDF>
+  </metadata>
+  <g
+     inkscape:label="Layer 1"
+     inkscape:groupmode="layer"
+     id="layer1"
+     transform="translate(-3.7199723,-50.587237)">
+    <ellipse
+       style="fill:#aa0000;fill-opacity:1;stroke:#313131;stroke-width:0.84230828;stroke-linecap:square;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:fill markers stroke"
+       id="path4518"
+       cx="151.00148"
+       cy="95.46405"
+       rx="42.394676"
+       ry="36.043724" />
+    <ellipse
+       style="fill:#ff6600;fill-opacity:1;stroke:#313131;stroke-width:1.03835058;stroke-linecap:square;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:fill markers stroke"
+       id="path4520"
+       cx="134.01062"
+       cy="106.35139"
+       rx="11.449168"
+       ry="9.3871698" />
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-weight:normal;font-size:7.73136568px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.19328415px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       x="122.82484"
+       y="85.048943"
+       id="text4524"
+       transform="scale(1.0263028,0.97437131)"><tspan
+         sodipodi:role="line"
+         id="tspan4522"
+         x="122.82484"
+         y="85.048943"
+         style="stroke-width:0.19328415px">loose-not-tight</tspan></text>
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-weight:normal;font-size:8.24097157px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.20602429px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       x="121.17614"
+       y="111.48331"
+       id="text4528"
+       transform="scale(1.0244129,0.97616888)"><tspan
+         sodipodi:role="line"
+         id="tspan4526"
+         x="121.17614"
+         y="111.48331"
+         style="stroke-width:0.20602429px">tight</tspan></text>
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-weight:normal;font-size:9.23775101px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.23094377px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       x="138.29958"
+       y="57.605762"
+       id="text4532"><tspan
+         sodipodi:role="line"
+         id="tspan4530"
+         x="138.29958"
+         y="57.605762"
+         style="stroke-width:0.23094377px">loose</tspan></text>
+    <ellipse
+       style="fill:#ff6600;fill-opacity:1;stroke:#313131;stroke-width:0.77813846;stroke-linecap:square;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:fill markers stroke"
+       id="path4520-3"
+       cx="47.706364"
+       cy="188.4809"
+       rx="41.060925"
+       ry="33.66584" />
+    <ellipse
+       style="fill:#aa0000;fill-opacity:1;stroke:#313131;stroke-width:0.84230828;stroke-linecap:square;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:fill markers stroke"
+       id="path4518-6"
+       cx="148.73363"
+       cy="185.11905"
+       rx="42.394676"
+       ry="36.043728" />
+    <ellipse
+       style="opacity:1;fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:#313131;stroke-width:1.03799999;stroke-linecap:square;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:fill markers stroke"
+       id="path4520-7"
+       cx="131.74277"
+       cy="196.00639"
+       rx="11.449168"
+       ry="9.3871698" />
+    <path
+       style="fill:none;fill-rule:evenodd;stroke:#313131;stroke-width:0.96499997;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+       d="m 172.67689,155.49333 0.022,59.25144 v 0"
+       id="path6035"
+       inkscape:connector-curvature="0" />
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-weight:normal;font-size:7.59049797px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.18976246px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       x="-120.80418"
+       y="237.36247"
+       id="text6039"
+       transform="rotate(-68.597684)"><tspan
+         sodipodi:role="line"
+         id="tspan6037"
+         x="-120.80418"
+         y="237.36247"
+         style="stroke-width:0.18976246px">prompt</tspan></text>
+    <g
+       id="g6195"
+       transform="matrix(0.81993875,0,0,0.81993875,14.073748,42.115491)">
+      <text
+         id="text6116"
+         y="76.772385"
+         x="-12.650279"
+         style="font-style:normal;font-weight:normal;font-size:6.03975105px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.15099378px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+         xml:space="preserve"><tspan
+           style="stroke-width:0.15099378px"
+           y="76.772385"
+           x="-12.650279"
+           id="tspan6114"
+           sodipodi:role="line">P(tight | loose) =</tspan></text>
+      <text
+         id="text6116-0"
+         y="74.334839"
+         x="40.189781"
+         style="font-style:normal;font-weight:normal;font-size:6.03975105px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.15099378px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+         xml:space="preserve"><tspan
+           style="stroke-width:0.15099378px"
+           y="74.334839"
+           x="40.189781"
+           id="tspan6114-9"
+           sodipodi:role="line">#tight - #tightPrompt</tspan></text>
+      <text
+         id="text6116-0-3"
+         y="80.975212"
+         x="38.349545"
+         style="font-style:normal;font-weight:normal;font-size:6.03975105px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.15099378px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+         xml:space="preserve"><tspan
+           style="stroke-width:0.15099378px"
+           y="80.975212"
+           x="38.349545"
+           id="tspan6114-9-6"
+           sodipodi:role="line">#loose - #loosePrompt</tspan></text>
+      <path
+         inkscape:connector-curvature="0"
+         id="path6154"
+         d="M 110.24868,75.767645 38.954532,76.101732"
+         style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.26458332px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1" />
+      <g
+         style="stroke-width:0.31677371;stroke-miterlimit:4;stroke-dasharray:none"
+         transform="matrix(0.89658997,0,0,1.0003463,-1.3869038,1.2054634)"
+         id="g6177">
+        <path
+           style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.31677371;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+           d="m -12.37872,70.403272 c 0.188988,-7.181546 12.94568427,-6.236607 12.94568427,-6.236607 0,0 10.96130973,1.417412 11.15029773,-1.984375"
+           id="path6158"
+           inkscape:connector-curvature="0" />
+        <path
+           style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.31677371;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+           d="M 35.813244,70.403272 C 35.624257,63.221726 22.86756,64.166665 22.86756,64.166665 c 0,0 -10.96131,1.417412 -11.150298,-1.984375"
+           id="path6158-0"
+           inkscape:connector-curvature="0" />
+      </g>
+      <text
+         id="text6181"
+         y="61.395809"
+         x="-5.8965478"
+         style="font-style:normal;font-weight:normal;font-size:6.06574249px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.15164356px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+         xml:space="preserve"><tspan
+           style="stroke-width:0.15164356px"
+           y="61.395809"
+           x="-5.8965478"
+           id="tspan6179"
+           sodipodi:role="line">&quot;fake rate&quot;</tspan></text>
+    </g>
+    <path
+       style="fill:none;fill-rule:evenodd;stroke:#313131;stroke-width:0.96499997;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+       d="m 28.877005,158.89512 0.022,59.25144 v 0"
+       id="path6035-6"
+       inkscape:connector-curvature="0" />
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-weight:normal;font-size:7.59049797px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.18976246px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       x="38.346554"
+       y="190.69165"
+       id="text6039-2"
+       transform="rotate(-0.43213102)"><tspan
+         sodipodi:role="line"
+         id="tspan6037-6"
+         x="38.346554"
+         y="190.69165"
+         style="stroke-width:0.18976246px">prompt</tspan></text>
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-weight:normal;font-size:6.17207098px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.15430179px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       x="-182.75136"
+       y="86.215508"
+       id="text6039-2-1"
+       transform="rotate(-68.597684)"><tspan
+         sodipodi:role="line"
+         id="tspan6037-6-8"
+         x="-182.75136"
+         y="86.215508"
+         style="stroke-width:0.15430179px">non-prompt</tspan></text>
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-weight:normal;font-size:7.59049797px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.18976246px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       x="119.53236"
+       y="177.85403"
+       id="text6039-2-1-7"
+       transform="rotate(-0.05072861)"><tspan
+         sodipodi:role="line"
+         id="tspan6037-6-8-9"
+         x="119.53236"
+         y="177.85403"
+         style="stroke-width:0.18976246px">non-prompt</tspan></text>
+    <path
+       style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.26458332;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:1.5874999, 0.26458332;stroke-dashoffset:0;stroke-opacity:1"
+       d="M 125.11012,100.83035 C 76.162201,137.30506 25.796875,159.88914 25.796875,159.88914"
+       id="path6254"
+       inkscape:connector-curvature="0"
+       sodipodi:nodetypes="cc" />
+    <path
+       style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.26458332;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:1.05833327, 0.26458332;stroke-dashoffset:0;stroke-opacity:1"
+       d="M 142.875,112.54762 C 116.60565,135.0372 83.15476,206.4747 83.15476,206.4747 v 0"
+       id="path6258"
+       inkscape:connector-curvature="0" />
+    <path
+       style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.26458332px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       d="m 193.14583,99.696427 c -6.80357,58.775303 -1.98437,83.154763 -1.98437,83.154763"
+       id="path6260"
+       inkscape:connector-curvature="0"
+       sodipodi:nodetypes="cc" />
+    <path
+       style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.26458332px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       d="m 108.66815,100.45238 c 6.04762,49.32589 -1.98437,80.31994 -1.98437,80.31994"
+       id="path6262"
+       inkscape:connector-curvature="0"
+       sodipodi:nodetypes="cc" />
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-weight:normal;font-size:8.24097157px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.20602429px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       x="50.707207"
+       y="157.64435"
+       id="text4528-2"
+       transform="scale(1.0244129,0.97616888)"><tspan
+         sodipodi:role="line"
+         id="tspan4526-0"
+         x="50.707207"
+         y="157.64435"
+         style="stroke-width:0.20602429px">tight</tspan></text>
+    <text
+       xml:space="preserve"
+       style="font-style:normal;font-weight:normal;font-size:7.73136568px;line-height:125%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.19328415px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+       x="117.23682"
+       y="151.38972"
+       id="text4524-2"
+       transform="scale(1.0263028,0.97437131)"><tspan
+         sodipodi:role="line"
+         id="tspan4522-3"
+         x="117.23682"
+         y="151.38972"
+         style="stroke-width:0.19328415px">loose-not-tight</tspan></text>
+  </g>
+</svg>

content/nuthesis.cls

@@ -1,251 +0,0 @@
-%%
-%% This is file `nuthesis.cls',
-%% generated with the docstrip utility.
-%%
-%% The original source files were:
-%%
-%% nuthesis.dtx  (with options: `class')
-%% This is a generated file.
-%% 
-%% Copyright (C) 2008 by Ned W. Hummel nhummel@gmail.com
-%% 
-%% This file may be distributed and/or modified under the conditions of
-%% the LaTeX Project Public License, either version 1.3c of this license
-%% or (at your option) any later version.  The latest version of this
-%% license is in:
-%% 
-%%    http://www.latex-project.org/lppl.txt
-%% 
-%% and version 1.3c or later is part of all distributions of LaTeX version
-%% 2006/05/20 or later.
-\NeedsTeXFormat{LaTeX2e}
-\ProvidesClass{nuthesis}
-    [2017/10/12 v0.7.2 University of Nebraska Thesis class]
-%% \CharacterTable
-%% {Upper-case    \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
-%%  Lower-case    \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
-%%  Digits        \0\1\2\3\4\5\6\7\8\9
-%%  Exclamation   \!     Double quote  \"     Hash (number) \#
-%%  Dollar        \$     Percent       \%     Ampersand     \&
-%%  Acute accent  \'     Left paren    \(     Right paren   \)
-%%  Asterisk      \*     Plus          \+     Comma         \,
-%%  Minus         \-     Point         \.     Solidus       \/
-%%  Colon         \:     Semicolon     \;     Less than     \<
-%%  Equals        \=     Greater than  \>     Question mark \?
-%%  Commercial at \@     Left bracket  \[     Backslash     \\
-%%  Right bracket \]     Circumflex    \^     Underscore    \_
-%%  Grave accent  \`     Left brace    \{     Vertical bar  \|
-%%  Right brace   \}     Tilde         \~}
-
-%% The ToC is required
-%% Uncomment these if need be
-
-\RequirePackage{ifthen}
-\RequirePackage{keyval}
-\RequirePackage{setspace}
-\RequirePackage{scrtime}
-\newboolean{nu@print}
-\newboolean{nu@single}
-\newcommand{\doctype}[1]{%
-  \gdef\nu@doctype{#1}}
-\newcommand{\nu@doctype}{}
-\newcommand{\degree}[1]{%
-  \gdef\nu@degree{#1}}
-\newcommand{\nu@degree}{}
-\newcommand{\degreeabbreviation}[1]{%
-  \gdef\nu@degreeabbreviation{#1}}
-\newcommand{\nu@degreeabbreviation}{}
-\newcommand{\major}[1]{%
-  \gdef\nu@major{#1}}
-\newcommand{\nu@major}{}
-\newcommand{\college}[1]{%
-  \gdef\nu@college{#1}}
-\newcommand{\nu@college}{Graduate College}
-\newcommand{\university}[1]{%
-  \gdef\nu@university{#1}}
-\newcommand{\nu@university}{University of Nebraska}
-\newcommand{\city}[1]{%
-  \gdef\nu@city{#1}}
-\newcommand{\nu@city}{Lincoln}
-\newcommand{\state}[1]{%
-  \gdef\nu@state{#1}}
-\newcommand{\nu@state}{Nebraska}
-\newcommand{\adviser}[1]{%
-  \gdef\nu@adviser{#1}}
-\newcommand{\adviserAbstract}[1]{%
-  \gdef\nu@adviserAbstract{#1}}
-\newcommand{\nu@adviser}{}
-\newcommand{\nu@adviserAbstract}{}
-\newcommand{\degreemonth}[1]{%
-  \gdef\nu@month{#1}}
-\newcommand{\nu@month}{}
-\newcommand{\degreeyear}[1]{%
-  \gdef\nu@year{#1}}
-\newcommand{\nu@year}{}
-\DeclareOption{testing}{%
-  \PassOptionsToPackage{showframe}{geometry}
-}
-\DeclareOption{single}{%
-  \setboolean{nu@single}{true}
-}
-
-\DeclareOption{double}{%
-  \setboolean{nu@single}{false}
-}
-\DeclareOption{print}{%
-  \setboolean{nu@print}{true}
-  \PassOptionsToPackage{bindingoffset=0.5in}{geometry}
-}
-\DeclareOption{electronic}{%
-\relax
-}
-\DeclareOption{phd}{%
-  \doctype{Dissertation}
-  \degree{Doctor of Philosophy}
-  \degreeabbreviation{Ph.D.}
-}
-
-\DeclareOption{edd}{%
-  \doctype{Dissertation}
-  \degree{Doctor of Education}
-  \degreeabbreviation{Ed.D.}
-}
-
-\DeclareOption{ms}{%
-  \doctype{Thesis}
-  \degree{Master of Science}
-  \degreeabbreviation{M.S.}
-}
-
-\DeclareOption{ma}{%
-  \doctype{Thesis}
-  \degree{Master of Art}
-  \degreeabbreviation{M.A.}
-}
-\DeclareOption*{%
-  \PassOptionsToClass{\CurrentOption}{memoir}
-}
-\ExecuteOptions{double,electronic,phd}
-\ProcessOptions
-\LoadClass[12pt,oneside]{memoir}
-\renewcommand{\chapnamefont}{\normalfont\large\bfseries}
-\renewcommand{\chapnumfont}{\normalfont\large\bfseries}
-\renewcommand{\chaptitlefont}{\large\bfseries}
-\renewcommand{\partnamefont}{\normalfont\large\bfseries}
-\renewcommand{\partnumfont}{\normalfont\large\bfseries}
-\renewcommand{\parttitlefont}{\normalfont\large\bfseries}
-\renewcommand{\secheadstyle}{\large\bfseries}
-\renewcommand{\subsecheadstyle}{\normalsize\bfseries}
-\renewcommand{\paraheadstyle}{\normalsize\bfseries}
-\renewcommand{\subparaheadstyle}{\normalsize\bfseries}
-\RequirePackage[letterpaper,margin=1in,includehead,nofoot]{geometry}
-\makepagestyle{nu@pagestyle}
-\makeoddhead{nu@pagestyle}%
-  {}{}{\normalfont\thepage}
-\makeevenhead{nu@pagestyle}%
-  {\normalfont\thepage}{}{}
-
-\makepagestyle{nu@pagestyleDraft}
-\makeoddhead{nu@pagestyleDraft}%
-  {\itshape\LaTeX{}ed at \thistime{} on \today}{}{\normalfont\thepage}
-\makeevenhead{nu@pagestyleDraft}%
-  {\normalfont\thepage}{}{\itshape\LaTeX{}ed at \thistime{} on \today}
-\ifdraftdoc
-  \aliaspagestyle{plain}{nu@pagestyleDraft}
-  \aliaspagestyle{empty}{nu@pagestyleDraft}
-%%  \aliaspagestyle{cleared}{nu@pagestyleDraft}
-  \pagestyle{nu@pagestyleDraft}
-\else
-  \aliaspagestyle{plain}{nu@pagestyle}
-%%  \aliaspagestyle{cleared}{nu@pagestyle}
-  \pagestyle{nu@pagestyle}
-\fi
-\renewcommand{\maketitle}{%
-\begin{center}%
-\MakeUppercase{\thetitle}\\[1\baselineskip]
-\singlespacing
-by\\[2\baselineskip]
-\theauthor\\[4\baselineskip]
-\MakeUppercase{A \nu@doctype}\\[4\baselineskip]
-Presented to the Faculty of\\[\baselineskip]
-The \nu@college{} at the \nu@university\\[\baselineskip]
-In Partial Fulfilment of Requirements\\[\baselineskip]
-For the Degree of \nu@degree\\[3\baselineskip]
-Major: \nu@major\\[3\baselineskip]
-Under the Supervision of \nu@adviser\\[3\baselineskip]
-\nu@city, \nu@state\\[1\baselineskip]
-\nu@month, \nu@year
-\end{center}
-\thispagestyle{empty}
-\cleardoublepage
-}
-\renewenvironment{abstract}{%
-  \pagestyle{empty}%
-  \begin{doublespacing}%
-    \begin{center}%
-      \MakeUppercase{\thetitle}\\[.5\baselineskip]
-      \theauthor, \nu@degreeabbreviation\\
-      \nu@university, \nu@year%
-    \end{center}%
-    \begin{flushleft}%
-      Adviser: \nu@adviserAbstract%
-    \end{flushleft}%
-  }{\par\end{doublespacing}\cleardoublepage}
-
-\newenvironment{copyrightpage}[1][Copyright]{%
-  \begin{center}%
-    \MakeUppercase{#1}\\
-    \copyright{} \nu@year, \theauthor%
-  \end{center}%
-  \ifthenelse{\boolean{nu@single}}{\begin{singlespacing}}{\begin{doublespacing}}%
-    }{\par%
-      \ifthenelse{\boolean{nu@single}}{\end{singlespacing}}{\end{doublespacing}}%
-  \cleardoublepage}
-
-\newenvironment{dedication}[1][Dedication]{%
-  \begin{center}%
-    \MakeUppercase{#1}%
-  \end{center}%
-  \ifthenelse{\boolean{nu@single}}{\begin{singlespacing}}{\begin{doublespacing}}%
-    }{\par%
-      \ifthenelse{\boolean{nu@single}}{\end{singlespacing}}{\end{doublespacing}}%
-  \cleardoublepage}
-
-\newenvironment{acknowledgments}[1][Acknowledgments]{%
-  \begin{center}
-    \MakeUppercase{#1}
-  \end{center}
-  \ifthenelse{\boolean{nu@single}}{\begin{singlespacing}}{\begin{doublespacing}}%
-    }{\par%
-      \ifthenelse{\boolean{nu@single}}{\end{singlespacing}}{\end{doublespacing}}%
-  \cleardoublepage}
-
-\newenvironment{grantinfo}[1][Grant Information]{%
-  \begin{center}
-    \MakeUppercase{#1}
-  \end{center}
-  \ifthenelse{\boolean{nu@single}}{\begin{singlespacing}}{\begin{doublespacing}}%
-    }{\par%
-      \ifthenelse{\boolean{nu@single}}{\end{singlespacing}}{\end{doublespacing}}%
-  \cleardoublepage}
-
-
-\let\nu@ToC\tableofcontents
-\renewcommand{\contentsname}{Table of Contents}
-\renewcommand{\tableofcontents}{\cleardoublepage\nu@ToC*}
-
-\let\nu@LoF\listoffigures
-\renewcommand{\listoffigures}{\cleardoublepage\nu@LoF}
-
-\let\nu@LoT\listoftables
-\renewcommand{\listoftables}{\cleardoublepage\nu@LoT}
-\maxsecnumdepth{subsubsection}
-\setsecnumdepth{subsubsection}
-\maxtocdepth{subsubsection}
-\let\backmatter\relax
-\AtBeginDocument{%
-\ifthenelse{\boolean{nu@single}}{\singlespacing}{\doublespacing}%
-}
-\endinput
-%%
-%% End of file `nuthesis.cls'.

content/thesis.tex

@@ -1,194 +0,0 @@
-%%
-%% This is file `skeleton.tex',
-%% generated with the docstrip utility.
-%%
-%% The original source files were:
-%%
-%% nuthesis.dtx  (with options: `skeleton')
-%% 
-
-% rubber: module pdftex
-
-%%
-%% For common degrees, you can use the class options:
-%% phd, edd, ms, ma
-%% phd is the default
-\documentclass[print]{nuthesis}
-
-%%%%%%%%% Preamble from pandoc
-\usepackage{lmodern}
-\usepackage{amssymb,amsmath}
-\usepackage{ifxetex,ifluatex}
-\usepackage{fixltx2e} % provides \textsubscript
-\usepackage[]{biblatex}
-\addbibresource{references.bib}
-
-\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
-  \usepackage[T1]{fontenc}
-  \usepackage[utf8]{inputenc}
-  \usepackage{textcomp} % provides euro and other symbols
-\else % if luatex or xelatex
-  \usepackage{unicode-math}
-  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
-\fi
-% use upquote if available, for straight quotes in verbatim environments
-\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
-% use microtype if available
-\IfFileExists{microtype.sty}{%
-\usepackage[]{microtype}
-\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
-}{}
-\IfFileExists{parskip.sty}{%
-\usepackage{parskip}
-}{% else
-\setlength{\parindent}{0pt}
-\setlength{\parskip}{6pt plus 2pt minus 1pt}
-}
-\usepackage{hyperref}
-\hypersetup{%
-            pdfborder={0 0 0},
-            breaklinks=true}
-\urlstyle{same}  % don't use monospace font for urls
-\usepackage{graphicx,grffile}
-\makeatletter
-\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
-\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
-\makeatother
-% Scale images if necessary, so that they will not overflow the page
-% margins by default, and it is still possible to overwrite the defaults
-% using explicit options in \includegraphics[width, height, ...]{}
-\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
-\setlength{\emergencystretch}{3em}  % prevent overfull lines
-\providecommand{\tightlist}{%
-  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
-\setcounter{secnumdepth}{0}
-% Redefines (sub)paragraphs to behave more like sections
-\ifx\paragraph\undefined\else
-\let\oldparagraph\paragraph%
-\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
-\fi
-\ifx\subparagraph\undefined\else
-\let\oldsubparagraph\subparagraph%
-\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
-\fi
-
-% set default figure placement to htbp
-\makeatletter
-\def\fps@figure{htbp}
-\makeatother
-
-\makeatletter
-\@ifpackageloaded{subfig}{}{\usepackage{subfig}}
-\@ifpackageloaded{caption}{}{\usepackage{caption}}
-\captionsetup[subfloat]{margin=0.5em}
-\AtBeginDocument{%
-\renewcommand*\figurename{Figure}
-\renewcommand*\tablename{Table}
-}
-% \AtBeginDocument{%
-% \renewcommand*\listfigurename{List of Figures}
-% \renewcommand*\listtablename{List of Tables}
-% }
-\@ifpackageloaded{float}{}{\usepackage{float}}
-\floatstyle{ruled}
-\@ifundefined{c@chapter}{\newfloat{codelisting}{h}{lop}}{\newfloat{codelisting}{h}{lop}[chapter]}
-\floatname{codelisting}{Listing}
-\newcommand*\listoflistings{\listof{codelisting}{List of Listings}}
-\makeatother
-
-%%%%%%%%% End Preamble from pandoc
-
-\begin{document}
-%% Start formatting the first few special pages
-%% frontmatter is needed to set the page numbering correctly
-\frontmatter
-
-\title{Measurement of the TTTT Cross Section at 13TeV}
-\author{Caleb Fangmeier}
-\adviser{Gregory Snow}
-\adviserAbstract{Professor Gregory Snow}
-\major{Physics and Astronomy}
-\degreemonth{TBD}
-\degreeyear{TBD}
-%%
-%% For most people the defaults will be correct, so they are commented
-%% out. To manually set these, just uncomment and make the needed
-%% changes.
-%% \college{Your college}
-%% \city{Your City}
-%%
-%% For most people the following can be changed with a class
-%% option. To manually set these, just uncomment the following and
-%% make the needed changes.
-%% \doctype{Thesis or Dissertation}
-%% \degree{Your degree}
-%% \degreeabbreviation{Your degree abbr.}
-%%
-%% Now that we know everything we need, we can generate the title page
-%% itself.
-%%
-\maketitle
-%%
-%% You have a maximum of 350 words for your abstract, which includes
-%% your title, name, etc.
-%%
-%% Required
-\begin{abstract}
-\include{00_Abstract}
-\end{abstract}
-
-%% Optional
-%% \begin{copyrightpage}
-%% \end{copyrightpage}
-
-%% Optional
-%% \begin{dedication}
-%% \end{dedication}
-
-%% Optional
-%% \begin{acknowledgments}
-%% \end{acknowledgments}
-
-%% Optional
-%% \begin{grantinfo}
-%% \end{grantinfo}
-%% The ToC is required
-%% Uncomment these if need be
-
-%% The ToC is required
-\tableofcontents
-%% Uncomment these if need be
-% \listoffigures
-% \listoftables
-%%
-%% ``Real'' beginning of the document.
-%% mainmatter is needed to set the page numbering correctly
-%%   mainmatter is needed after the ToC, (LoF, and LoT) to set the
-%%   page numbering correctly for the main body
-\mainmatter%
-
-%% Thesis goes here
-
-\include{01_introduction}
-\include{02_standard_model}
-\include{03_theory}
-
-%% backmatter is needed at the end of the main body of your thesis to
-%% set up page numbering correctly for the remainder of the thesis
-\backmatter%
-
-%% Start the correct formatting for the appendices
-\appendix
-
-%% Appendices go here (if you have them)
-
-%% Bibliography goes here (You better have one)
-%% BibTeX is your friend
-\printbibliography%
-
-%% Index go here (if you have one)
-\end{document}
-
-\endinput
-%%
-%% End of file `skeleton.tex'.

convert.py

@@ -1,48 +1,31 @@
 #!/usr/bin/env python3
 import os
 import sys
-import re
+from re import match
 from subprocess import run
-from os.path import splitext
-from glob import glob
-
-# title_re = re.compile(r'^# (.*)$', re.MULTILINE)
-# tex_re = re.compile(r'\\begin{document}(.*)\\end{document}', re.MULTILINE | re.DOTALL)
-
-
-def parse_title(infilename):
-    # Find chapter title
-    with open(infilename) as f:
-        matches = title_re.findall(f.read())
-    if matches:
-        return matches[0]
-    else:
-        return splitext(infilename.split('/')[-1])[0]
+from os import listdir, rename
+from shutil import copyfile
+from os.path import splitext, join
 
 
 def make_tex(infilename):
-    # title = parse_title(infilename)
     outfilename = splitext(infilename)[0]+'.tex'
     run(('pandoc', '--biblatex', '-F', 'pandoc-crossref', '-s', infilename, '-o', outfilename,
          '--metadata=bibliography:references.bib',
          '--template=chapter',
          ))
     with open(outfilename, 'r') as f:
-        full = f.read()
-        # body = tex_re.findall(full)[0]
-        body = full
-        # body = body.replace('section{'+title+'}', 'chapter{'+title+'}')
+        body = f.read()
         body = body.replace(r'\printbibliography', '')
     with open(outfilename, 'w') as f:
         f.write(body)
 
 
 def make_html(infilename):
-    # title = parse_title(infilename)
     outfilename = splitext(infilename)[0]+'.html'
     run(('pandoc', '-F', 'pandoc-crossref', '-F', 'pandoc-citeproc', '-s', infilename, '-o', outfilename,
+         '--mathjax',
          '--metadata=linkReferences:true',
-         # f'--metadata=pagetitle:{title}',
          '--metadata=bibliography:references.bib',
          '--metadata=citation-style:american-physics-society.csl',
          '--template=chapter',
@@ -53,12 +36,22 @@ def main():
     if len(sys.argv) != 2 or sys.argv[1] not in ('html', 'tex'):
         print('usage: ./convert.py [html|tex]')
         sys.exit(1)
-    os.chdir('content')
-    for infilename in glob('*_*.md'):
-        if sys.argv[1] == 'html':
+
+    for fname in listdir('content'):
+        if match(r'.*\.md', fname):
+            copyfile(join('content', fname), join('build', fname))
+
+    os.chdir('build')
+    fmt = sys.argv[1]
+    for infilename in listdir('.'):
+        if not match(r'.*\.md', infilename):
+            continue
+        print(f'Converting {infilename} to {fmt}...', end='', flush=True)
+        if fmt == 'html':
             make_html(infilename)
         else:
             make_tex(infilename)
+        print('Done')
 
 
 if __name__ == '__main__':

develop_server.sh

@@ -7,7 +7,7 @@ PELICAN=${PELICAN:-pelican}
 PELICANOPTS=
 
 BASEDIR=$(pwd)
-INPUTDIR=$BASEDIR/content
+INPUTDIR=$BASEDIR/build
 OUTPUTDIR=$BASEDIR/output
 CONFFILE=$BASEDIR/pelicanconf.py
 

elegant

@@ -1 +1 @@
-Subproject commit 588b8e5badf59b4a7ae87e352b25b85a59dd1d42
+Subproject commit 5cddb411a417e3489eb673810a81bca3c7e43fcd

pelicanconf.py

@@ -6,8 +6,6 @@ AUTHOR = 'Caleb Fangmeier'
 SITENAME = "Caleb Fangmeier's Doctoral Thesis"
 SITEURL = 'thesis.fangmeier.tech'
 
-PATH = 'content'
-
 TIMEZONE = 'America/Chicago'
 
 DEFAULT_LANG = 'en'

requirements.txt

@@ -0,0 +1,12 @@
+beautifulsoup4==4.6.1
+blinker==1.4
+docutils==0.14
+feedgenerator==1.9
+Jinja2==2.10
+MarkupSafe==1.0
+pelican==3.7.1
+Pygments==2.2.0
+python-dateutil==2.7.3
+pytz==2018.5
+six==1.11.0
+Unidecode==1.0.22