Makefile is now pretty.

Makefile

-.PHONY: build install clean build_docker push_docker clean_test test_simu test_det test_val real analyses_30Bloom analyses_263Bloom
-
+# -----------------------------------------------------------------------
+#   Build and install things
+# -----------------------------------------------------------------------
+.PHONY: build
 build:
 	jbuilder build
 
+.PHONY: install
 install:
 	jbuilder install
 
-clean:
-	rm -rf _build
-	rm -rf example/_bistro
-	rm -rf example/outdir
-
+.PHONY: build_docker
 build_docker:
 	@for dir in ./etc/docker/*; \
 	do\
@@ -19,6 +18,7 @@ build_docker:
 		cd - ; \
 	done
 
+.PHONY: push_docker
 push_docker:
 	@for dir in ./etc/docker/*; \
 	do\
@@ -27,45 +27,65 @@ push_docker:
 		cd - ; \
 	done
 
+# -----------------------------------------------------------------------
+#   Tests and experiments
+# -----------------------------------------------------------------------
+.PHONY: test_simu
 test_simu:
 	cd example && \
 	reviewphiltrans simulation --outdir outdir --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4 && \
 	mv dag.dot dagtest_sim.dot && \
 	dot -Tsvg dagtest_sim.dot -o dagtest_sim.svg
 
+.PHONY: test_det
 test_det:
 	cd example && \
 	reviewphiltrans detection --outdir outdir/detection --indir outdir/data --preview --np 4 && \
 	mv dag.dot dagtest_det.dot && \
 	dot -Tsvg dagtest_det.dot -o dagtest_det.svg
 
+.PHONY: test_val
 test_val:
 	cd example && \
 	reviewphiltrans validation --outdir outdir_validation --indir real_data --tree-dir trees --profile-fn aa_fitness/tiragesBloomK30.tsv --preview --np 4 && \
 	mv dag.dot dagtest_val.dot && \
 	dot -Tsvg dagtest_val.dot -o dagtest_val.svg
 
+.PHONY: real
 real:
 	cd example && \
 	reviewphiltrans detection --outdir outdir_real_data --indir real_data --preview --np 4 && \
 	mv dag.dot dagtest_real.dot && \
 	dot -Tpdf dagtest_real.dot -o dagtest_real.pdf
 
+.PHONY: analyses_30Bloom
 analyses_30Bloom:
 	cd example && \
 	reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30 --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 && \
 	mv dag.dot daganalyses_tiragesBloomK30.dot
 
+.PHONY: analyses_263Bloom
 analyses_263Bloom:
 	cd example && \
 	reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 && \
 	mv dag.dot daganalyses_263SelectedProfiles.dot
 
+# -----------------------------------------------------------------------
+#   Cleaning and formatting
+# -----------------------------------------------------------------------
+.PHONY: clean
+clean:
+	rm -rf _build
+	rm -rf example/_bistro
+	rm -rf example/outdir
+
+.PHONY: clean_test
 clean_test:
 	rm -rf example/_bistro
 	rm -rf example/outdir
 	rm -rf example/report.log
 	rm -rf example/dot.dag
 
+.PHONY: format
 format:
 	ocp-indent -i lib/*.ml lib/*.mli app/*.ml