Scaffold out manuscript along with primary figures

.gitignore

@@ -18,6 +18,9 @@ nextclade_sars-cov-2_root-sequence.json
 embeddings_pretrained.tsv
 embeddings_fine_tuned.tsv
 
+# Compiled manuscript files
+fitness_flux.pdf
+
 # Errors from tests
 *.err
 
@@ -33,6 +36,14 @@ environment*
 .tox/
 .cache/
 
+# LaTeX intermediaries #
+########################
+*.aux
+*.log
+*.bbl
+*.blg
+*.out
+
 # Compiled source #
 ###################
 *.com

manuscript/Rakefile

@@ -0,0 +1,153 @@
+# Rakefile to collect all .tex files in a directory and run `pdflatex` and `bibtex` as needed to 
+# produce PDF output.  If a .tex file is updated `pdflatex -draftmode` will be run to produce new 
+# .aux and .log files.  These are used to determine whether `bibtex` needs to be run.  If so `bibtex` 
+# will always need to be followed by `pdflatex -draftmode`.  With fully updated .aux and .bbl in 
+# hand, a final `pdflatex` is run.  The only hole in the logic I've found is that, when making a 
+# small revision, this will run `pdflatex -draftmode` then `pdflatex` when only `pdflatex` is 
+# required.
+#
+# Run `rake` to compile PDFs and `rake clean` to remove the intermediary cruft
+
+basedir = Dir.getwd 
+
+TEX = FileList["**/*.tex"]
+AUX = TEX.ext("aux")
+BBL = TEX.ext("bbl")
+BLG = TEX.ext("blg")
+LOG = TEX.ext("log")
+OUT = TEX.ext("out")
+PDF = TEX.ext("pdf")
+
+require 'rake/clean'
+CLEAN.include(AUX)
+CLEAN.include(BBL)
+CLEAN.include(BLG)
+CLEAN.include(LOG)
+CLEAN.include(OUT)
+CLOBBER.include(PDF)
+
+desc "Full compile"
+task :default => PDF 
+
+desc "LaTeX aux"
+rule ".aux" => ".tex" do |t|
+	prefix = t.name.pathmap("%n")
+	dir = t.name.pathmap("%d")
+	Dir.chdir(dir)
+	puts "pdflatex -draftmode #{prefix}"
+	`pdflatex -draftmode #{prefix}`
+	Dir.chdir(basedir)
+end
+
+desc "LaTeX log"
+rule ".log" => ".tex" do |t|
+	prefix = t.name.pathmap("%n")
+	dir = t.name.pathmap("%d")
+	Dir.chdir(dir)	
+	puts "pdflatex -draftmode #{prefix}"
+	`pdflatex -draftmode #{prefix}`
+	Dir.chdir(basedir)	
+end
+
+desc "LaTeX compile"
+# require log file and proceed if references are incomplete
+rule ".pdf" => [".aux", ".bbl", ".log", ".tex"]  do |t|
+	prefix = t.name.pathmap("%n")
+	dir = t.name.pathmap("%d")
+	Dir.chdir(dir)		
+	puts "pdflatex #{prefix}"
+	`pdflatex #{prefix}`
+	Dir.chdir(basedir)		
+end
+
+desc "BibTex compile"
+# look for .bib file in top-level directory
+rule ".bbl" => [".aux", ".log", ".tex"]  do |t|
+	prefix = t.name.pathmap("%n")
+	dir = t.name.pathmap("%d")
+	Dir.chdir(dir)			
+	if cite?(prefix)
+		puts "bibtex #{prefix}"
+		`bibtex #{prefix}`
+		puts "pdflatex -draftmode #{prefix}"
+		`pdflatex -draftmode #{prefix}`
+	end
+	Dir.chdir(basedir)		
+end
+
+desc "Look at log file and check if references are complete"
+def ref?(string)
+	dirty = false
+	file = File.open("#{string}.log", "r")
+	m = file.read.match(/LaTeX Warning: There were undefined references|LaTeX Warning: Label(s) may have changed. Rerun to get|^LaTeX Warning: Reference/)
+	file.close
+	if m != nil
+		puts m
+		dirty = true
+	end	
+	return dirty
+end
+
+desc "Are citations up to date?"
+def cite?(string)
+	dirty = false
+	if File.exists?("#{string}.bbl")
+		if cite_missing(string) == true
+			dirty = true
+		else
+			aux_list = cite_aux(string)
+			bbl_list = cite_bbl(string)
+			extra = (aux_list - bbl_list).length
+			missing = (bbl_list - aux_list).length
+			if extra > 0 || missing > 0
+				dirty = true
+			end
+		end
+	else
+		dirty = true
+	end
+	return dirty
+end
+
+desc "Look at log file and check if citations are complete"
+def cite_missing(string)
+	dirty = false
+	file = File.open("#{string}.log", "r")
+	m = file.read.match(/^LaTeX Warning: Citation/)
+	file.close
+	if m != nil
+		puts m
+		dirty = true
+	end	
+	return dirty
+end
+
+desc "Find citations in .aux"
+def cite_aux(string)
+	list = Array.new
+	file = File.open("#{string}.aux", "r")
+	cites = file.read.scan(/\\citation{([^\}]+)}/)
+	file.close
+	if cites != nil
+		cites.each {|m|
+			list += m[0].split(",")
+		}
+	end	
+	list.uniq!
+	return list
+end
+
+desc "Find citations in .bbl"
+def cite_bbl(string)
+	list = Array.new
+	file = File.open("#{string}.bbl", "r")
+	cites = file.read.scan(/\\bibitem{([^\}]+)}/)
+	file.close
+	if cites != nil
+		cites.each {|m|
+			list += m[0].split(",")
+		}
+	end	
+	list.uniq!
+	return list
+end