mustache preprocessing

1 files changed, 39 insertions, 13 deletions

diff --git a/Makefile b/Makefile
index 421d75e..a95eb32 100644
--- a/Makefile
+++ b/Makefile
@@ -1,16 +1,16 @@
 # Manuscript
-# please install pandoc-scholar (https://github.com/pandoc-scholar/pandoc-scholar) in the pandoc-scholar directory or point PANDOC_SCHOLAR_PATH to your installation
+# Requirements:
+# pandoc-scholar (https://github.com/pandoc-scholar/pandoc-scholar) in PANDOC_SCHOLAR_PATH
+# pandoc-placetable (https://github.com/mb21/pandoc-placetable)
 
-ARTICLE_FILE          = mutagenicity.md
+ARTICLE_FILE          = mutagenicity.mustache.md
 PANDOC_SCHOLAR_PATH   = pandoc-scholar
 OUTFILE_PREFIX        = mutagenicity
-DEFAULT_EXTENSIONS    = latex pdf docx #odt epub html
-PANDOC_WRITER_OPTIONS = --filter=pandoc-citeproc
-#PANDOC_WRITER_OPTIONS = --filter=pandoc-placetable --filter=pandoc-citeproc
+DEFAULT_EXTENSIONS    = pdf #latex docx html #odt epub
+#PANDOC_WRITER_OPTIONS = --filter=panpipe --filter=pandoc-placetable --filter=pandoc-citeproc -M tmpvar=test
+PANDOC_WRITER_OPTIONS = --filter=pandoc-crossref --filter=pandoc-placetable --filter=pandoc-citeproc 
 TEMPLATE_FILE_LATEX   = pandoc-scholar.latex
 
-include $(PANDOC_SCHOLAR_PATH)/Makefile
-
 # Lazar
 
 LAZAR_DIR = ../lazar
@@ -28,29 +28,55 @@ CONFUSION_MATRICES_DIR = 10-fold-crossvalidations/confusion-matrices
 R_CV_DIR = 10-fold-crossvalidations/R
 TENSORFLOW_CV_DIR = 10-fold-crossvalidations/tensorflow
 
-#tables = tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv
+TABLES = tables/r-summary.csv tables/tf-summary.csv tables/lazar-summary.csv tables/R-SVM.csv tables/R-RF.csv tables/R-DL.csv tables/tensorflow-all.csv tables/tensorflow-selected.csv tables/lazar-all.csv tables/lazar-high-confidence.csv tables/lazar-padel-all.csv tables/lazar-padel-high-confidence.csv
+
+R_SUMMARIES = $(SUMMARIES_DIR)/R-SVM.json $(SUMMARIES_DIR)/R-RF.json $(SUMMARIES_DIR)/R-DL.json
+TF_SUMMARIES = $(SUMMARIES_DIR)/tensorflow-all.json $(SUMMARIES_DIR)/tensorflow-selected.json
+LAZAR_SUMMARIES = $(SUMMARIES_DIR)/lazar-all.json $(SUMMARIES_DIR)/lazar-high-confidence.json $(SUMMARIES_DIR)/lazar-padel-all.json $(SUMMARIES_DIR)/lazar-padel-high-confidence.json
 
-SUMMARIES = $(SUMMARIES_DIR)/R-SVM.csv $(SUMMARIES_DIR)/R-RF.csv $(SUMMARIES_DIR)/R-DL.csv $(SUMMARIES_DIR)/tensorflow-all.csv $(SUMMARIES_DIR)/tensorflow-selected.csv $(SUMMARIES_DIR)/lazar-all.csv $(SUMMARIES_DIR)/lazar-high-confidence.csv $(SUMMARIES_DIR)/lazar-padel-all.csv $(SUMMARIES_DIR)/lazar-padel-high-confidence.csv
+SUMMARIES = $(R_SUMMARIES) $(TF_SUMMARIES) $(LAZAR_SUMMARIES)
 
 CONFUSION_MATRICES = $(CONFUSION_MATRICES_DIR)/R-SVM.csv $(CONFUSION_MATRICES_DIR)/R-RF.csv $(CONFUSION_MATRICES_DIR)/R-DL.csv $(CONFUSION_MATRICES_DIR)/tensorflow-all.csv $(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv $(CONFUSION_MATRICES_DIR)/lazar-all.csv $(CONFUSION_MATRICES_DIR)/lazar-high-confidence.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-all.csv $(CONFUSION_MATRICES_DIR)/lazar-padel-high-confidence.csv
 
 DATA = data/mutagenicity.sdf data/mutagenicity.csv data/mutagenicity-fingerprints.csv
 
-all: $(SUMMARIES) $(DATA) #$(tables)
+all: $(DATA) $(TABLES) mutagenicity.pdf $(SUMMARIES_DIR)/results.json
+#all: $(SUMMARIES) $(DATA) $(TABLES) mutagenicity.pdf
+include $(PANDOC_SCHOLAR_PATH)/Makefile
 export: $(DATA) 
 
+mutagenicity.mustache.md: $(SUMMARIES_DIR)/results.json mutagenicity.md
+	mustache $^ > $@
+
+# tables
+
+tables/r-summary.csv: $(R_SUMMARIES)
+	scripts/summaries2table.rb $^ > $@
+
+tables/tf-summary.csv: $(TF_SUMMARIES)
+	scripts/summaries2table.rb $^ > $@
+
+tables/lazar-summary.csv: $(LAZAR_SUMMARIES)
+	scripts/summaries2table.rb $^ > $@
+
+tables/%.csv: $(CONFUSION_MATRICES_DIR)/%.csv
+	scripts/confusion-matrix2table.rb $< > $@
+
 # summaries
 
-$(SUMMARIES_DIR)/%.csv: $(CONFUSION_MATRICES_DIR)/%.csv
+$(SUMMARIES_DIR)/results.json: $(SUMMARIES)
+	scripts/results.rb $^ > $@
+
+$(SUMMARIES_DIR)/%.json: $(CONFUSION_MATRICES_DIR)/%.csv
 	scripts/confusion-matrix-summary.rb $< > $@
 
 # confusion matrices
 
 ## tensorflow
-$(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv: $(TENSORFLOW_CV_DIR)/pred.csv
+$(CONFUSION_MATRICES_DIR)/tensorflow-selected.csv: $(TENSORFLOW_CV_DIR)/pred.sorted.csv
 	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
 
-$(CONFUSION_MATRICES_DIR)/tensorflow-all.csv: $(TENSORFLOW_CV_DIR)/pred_ext.csv
+$(CONFUSION_MATRICES_DIR)/tensorflow-all.csv: $(TENSORFLOW_CV_DIR)/pred_ext.sorted.csv
 	scripts/cv-tensorflow-confusion-matrix.rb $< > $@
 
 ## R