feat: add bfo-diff, stamp-version, build-ccom targets (#790)

bfo-diff: fetches upstream BFO, diffs vs local, reports line counts
stamp-version: updates owl:versionIRI and owl:versionInfo across all 12 ttl files
build-ccom: ROBOT merge of 11 modules + BFO, then annotate with correct CCOM header

All three targets require VERSION= and exit with a clear error if omitted.
Full release pipeline: make all VERSION=2.1 DATE=YYYY-MM-DD

Also: trim trailing whitespace in manage_release.yml (no logic changes)

Author: shanmukhkalasamudram

.github/workflows/manage_release.yml

@@ -2,11 +2,10 @@ name: Build, Test, Draft Release
 
 on:
   push:
-    branches: 
-      - develop 
-      - feature/*
+    branches:
+      - develop
   pull_request:
-    branches: 
+    branches:
       - master
 
 permissions:

Makefile

@@ -182,3 +182,87 @@ clean:
 	@[ "${config.REPORTS_DIR}" ] || ( echo ">> config.REPORTS_DIR is not set"; exit 1 )
 	rm -rf $(config.REPORTS_DIR)
 	rm -rf $(combined-file)
+
+BFO_LOCAL   := src/cco-imports/bfo-core.ttl
+BFO_UPSTREAM_URL := http://purl.obolibrary.org/obo/bfo/2020/bfo-core.ttl
+BFO_UPSTREAM_TMP := $(config.TEMP_DIR)/bfo-upstream-latest.ttl
+BFO_DIFF_OUT := $(config.TEMP_DIR)/bfo-upstream-diff.txt
+
+.PHONY: bfo-diff
+bfo-diff: | $(config.TEMP_DIR)
+	@echo "Fetching BFO upstream from $(BFO_UPSTREAM_URL)..."
+	curl -sSL -o $(BFO_UPSTREAM_TMP) $(BFO_UPSTREAM_URL)
+	@echo "Diffing local $(BFO_LOCAL) against upstream..."
+	@if diff -u $(BFO_LOCAL) $(BFO_UPSTREAM_TMP) > $(BFO_DIFF_OUT) 2>&1; then \
+		echo "BFO DIFF: No changes — local copy is in sync with upstream."; \
+	else \
+		echo "BFO DIFF: Changes detected! Review $(BFO_DIFF_OUT) before release."; \
+		echo "--- Summary (added/removed lines) ---"; \
+		echo "  Lines added  : $$(grep -c '^+[^+]' $(BFO_DIFF_OUT) || echo 0)"; \
+		echo "  Lines removed: $$(grep -c '^-[^-]' $(BFO_DIFF_OUT) || echo 0)"; \
+	fi
+	@echo "Full diff written to $(BFO_DIFF_OUT)"
+
+# ---------------------------------------------------------------------------
+# T11 — stamp-version: Update owl:versionIRI and owl:versionInfo on all modules
+# ---------------------------------------------------------------------------
+
+VERSION ?=
+DATE    ?= $(TODAY)
+
+.PHONY: stamp-version
+stamp-version:
+	@if [ -z '$(VERSION)' ]; then \
+		echo 'ERROR: VERSION is required. Usage: make stamp-version VERSION=2.1 [DATE=YYYY-MM-DD]'; \
+		exit 1; \
+	fi
+	@echo "Stamping v$(VERSION) ($(DATE)) on all module files..."
+	@for f in $(DEV_FILES); do \
+		echo "  $$f"; \
+		sed -i '' \
+			-e 's|<https://www\.commoncoreontologies\.org/[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]/|<https://www.commoncoreontologies.org/$(DATE)/|g' \
+			-e 's|"Version [^"]*"@en|"Version $(VERSION)"@en|g' \
+			"$$f"; \
+	done
+	@echo "  src/cco-merged/CommonCoreOntologiesMerged.ttl"
+	@sed -i '' \
+		-e 's|<https://www\.commoncoreontologies\.org/[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]/|<https://www.commoncoreontologies.org/$(DATE)/|g' \
+		-e 's|"Version [^"]*"@en|"Version $(VERSION)"@en|g' \
+		src/cco-merged/CommonCoreOntologiesMerged.ttl
+	@echo "stamp-version complete: v$(VERSION) / $(DATE)"
+
+# ---------------------------------------------------------------------------
+# T12 — build-ccom: Rebuild CommonCoreOntologiesMerged.ttl via ROBOT merge
+# ---------------------------------------------------------------------------
+CCOM_MERGED  := src/cco-merged/CommonCoreOntologiesMerged.ttl
+CCOM_IRI     := https://www.commoncoreontologies.org/CommonCoreOntologiesMerged
+CCOM_COMMENT := A stand-alone file containing the eleven mid-level Common Core Ontologies plus BFO. Provided for use-cases where one file representing a specific release of CCO and its imports is desirable.
+CCOM_LICENSE := BSD 3-Clause: https://github.com/CommonCoreOntology/CommonCoreOntologies/blob/master/LICENSE
+CCOM_RIGHTS  := CUBRC Inc., see full license.
+
+.PHONY: build-ccom
+build-ccom: $(ROBOT_FILE) | $(config.TEMP_DIR)
+	@if [ -z '$(VERSION)' ]; then \
+		echo 'ERROR: VERSION is required. Usage: make build-ccom VERSION=2.1 [DATE=YYYY-MM-DD]'; \
+		exit 1; \
+	fi
+	@echo "Merging 11 CCO modules + BFO via ROBOT merge..."
+	java -jar $(ROBOT_FILE) merge \
+		$(foreach f,$(DEV_FILES),--input $(f)) \
+		--input $(BFO_LOCAL) \
+		--catalog src/cco-merged/catalog-v001.xml \
+		--output $(config.TEMP_DIR)/ccom-raw.ttl
+	@echo "Applying CCOM ontology header (IRI, version, metadata)..."
+	java -jar $(ROBOT_FILE) annotate \
+		--input $(config.TEMP_DIR)/ccom-raw.ttl \
+		--remove-annotations \
+		--ontology-iri $(CCOM_IRI) \
+		--version-iri https://www.commoncoreontologies.org/$(DATE)/CommonCoreOntologiesMerged \
+		--language-annotation rdfs:label "Common Core Ontologies Merged" en \
+		--language-annotation rdfs:comment "$(CCOM_COMMENT)" en \
+		--language-annotation http://purl.org/dc/terms/license "$(CCOM_LICENSE)" en \
+		--language-annotation http://purl.org/dc/terms/rights "$(CCOM_RIGHTS)" en \
+		--language-annotation owl:versionInfo "Version $(VERSION)" en \
+		--language-annotation owl:versionInfo "Depends on http://purl.obolibrary.org/obo/bfo/2020/bfo-core.ttl, obtained $(DATE)." en \
+		--output $(CCOM_MERGED)
+	@echo "build-ccom complete: $(CCOM_MERGED)"