Initial

Makefile

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+.PHONY: all clean clean_notebooks clean_report
+
+all: output/manuscript.pdf
+
+# List of plot image targets
+PLOTS = output/plots/bell_violation.png\
+		output/plots/fidelity_dist.png\
+		output/plots/detector_comparison.png\
+		output/plots/visibility_distance.png\
+		output/plots/world_map.png\
+		output/plots/coincidence_rates.png\
+		output/plots/temperature_effects.png
+
+# List of table targets
+TABLES = output/tables/summary.tex\
+		output/tables/laboratories.tex
+
+# Final PDF depends on manuscript source, plots, and tables
+output/manuscript.pdf: report/manuscript.tex $(PLOTS) $(TABLES)
+	cd report\
+	&& pdflatex manuscript.tex\
+	&& pdflatex manuscript.tex\
+	&& mv manuscript.pdf ../output/manuscript.pdf
+
+# Base data generation from raw data
+data/base/data.csv: notebooks/make_basedata.ipynb data/raw/experimental_data.csv
+	cd notebooks\
+	&& papermill make_basedata.ipynb /dev/null
+
+# Pattern rule for tables
+$(TABLES): output/tables/%.tex: notebooks/tab_%.ipynb data/base/data.csv
+	cd notebooks\
+	&& papermill $(notdir $<) /dev/null
+
+# Pattern rule for plots
+$(PLOTS): output/plots/%.png: notebooks/plot_%.ipynb data/base/data.csv
+	cd notebooks\
+	&& papermill $(notdir $<) /dev/null
+
+# Clean up generated files
+clean: clean_notebooks clean_report
+	rm -f data/base/data.csv data/base/data.pkl
+	rm -f output/plots/*.png
+	rm -f output/tables/*.tex
+	rm -f output/manuscript.pdf
+
+# Clear notebook outputs
+clean_notebooks:
+	jupyter nbconvert notebooks/*.ipynb --clear-output --inplace
+
+# Clean up LaTeX auxiliary files
+clean_report:
+	rm -f report/manuscript.aux
+	rm -f report/manuscript.log
+	rm -f report/manuscript.out
+	rm -f report/manuscript.bbl
+	rm -f report/manuscript.blg