From 30ea34d0728003732a0e7069e2bf15f517b79f10 Mon Sep 17 00:00:00 2001
From: "Mark A. Miller" <MAM@lbl.gov>
Date: Thu, 16 Jan 2025 16:14:31 -0500
Subject: [PATCH] clean makefiel target. `make all` works after using it.

---
 src/envo/Makefile       |  3 ++-
 src/envo/clean.Makefile | 43 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+), 1 deletion(-)
 create mode 100644 src/envo/clean.Makefile

diff --git a/src/envo/Makefile b/src/envo/Makefile
index 78d66880..a52928c3 100644
--- a/src/envo/Makefile
+++ b/src/envo/Makefile
@@ -578,4 +578,5 @@ fill: envo-edit.csv
 #modules/%.tsv:
 #	blip-findall -i patterns/spec.obo  -consult pmaker.pro -r envo -r chebi -r pato pattern_$*/3 -no_pred -label -use_tabs > $@
 
-include envo.Makefile
\ No newline at end of file
+include envo.Makefile
+include clean.Makefile
diff --git a/src/envo/clean.Makefile b/src/envo/clean.Makefile
new file mode 100644
index 00000000..a7fa0376
--- /dev/null
+++ b/src/envo/clean.Makefile
@@ -0,0 +1,43 @@
+# prototype from ChatGPT
+
+.PHONY: clean
+
+clean:
+	# Remove temporary and intermediate files
+	rm -rf $(TMPDIR)/
+	rm -rf tmp/
+	cp reports/report_profile_edit.txt report_profile_edit.txt
+	rm -rf reports/* # need to keep reports/report_profile_edit.txt
+	cp report_profile_edit.txt reports/report_profile_edit.txt
+	rm -rf modules/*.tmp.owl
+	rm -rf modules/*.obo
+	#rm -rf modules/*.owl # how are these recreated?
+	rm -rf mirror/*.owl
+	#rm -rf imports/*.owl # how are these recreated?
+	rm -rf imports/*.obo
+	rm -rf patterns/matches/logical/
+	rm -rf patterns/matches/annotations/
+
+	# Remove generated ontology files
+	rm -f $(ONT).owl $(ONT).obo $(ONT).json
+	rm -f $(ONT)-full.owl $(ONT)-full.obo $(ONT)-full.json
+	rm -f $(ONT)-base.owl $(ONT)-base.obo $(ONT)-base.json
+	#rm -f $(SRC) $(PRE_SRC) # $(SRC) = ??? ; $(PRE_SRC) = ???
+
+	# Remove subset files
+	rm -f subsets/*.owl subsets/*.obo subsets/*.json subsets/*.tsv
+
+	# Remove downloaded or mirrored external ontologies
+	rm -rf mirror/
+	rm -f GO.xrf_abbs
+
+	# Remove any temporary downloads or caches
+	rm -rf diffs/
+	rm -f *.tmp
+	rm -f *.log
+
+	# Optional: Remove release artifacts if generated
+	rm -rf $(RELEASEDIR)/$(ONT).owl $(RELEASEDIR)/$(ONT).obo $(RELEASEDIR)/$(ONT).json
+	rm -rf $(RELEASEDIR)/subsets/
+	rm -rf $(RELEASEDIR)/mappings/
+	rm -rf $(RELEASEDIR)/imports/