Move virtual environment construction to root directory

The Protege catalog XML construction design involves review of the
transitive `owl:imports` closure of UCO's graph files.  To do this,
RDFLib needs to be available in a Python virtual environment before
descending into the `/ontology` directory.  Before this patch, a virtual
environment with RDFLib was constructed in `/tests` for testing, but not
for other ontology-related maintenance.

This patch moves the virtual environment construction to the UCO
repository root directory, and sets the dependency order of `all` and
`check` to include `/venv` being built before descent into `/ontology`
and `/tests.  All paths referencing `/tests/venv` under `/tests` have
been updated.

As one bit of code upgrading, the `PYTHON3` selector snippet, originally
written before Python 3.10's release, now looks only for the default
Python 3 if not supplied when calling Make (e.g. with
`make PYTHON3=python3.11 check`).

This patch isolates its effects to moving the virtual environment.
A follow-on patch will integrate catalog construction using the new
placement.

References:
* #449

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>

.gitignore

@@ -2,3 +2,6 @@
 .*.ttl
 .git_submodule_init.done.log
 .lib.done.log
+.venv.done.log
+_*
+venv

Makefile

@@ -13,6 +13,8 @@
 
 SHELL := /bin/bash
 
+PYTHON3 ?= $(shell which python3)
+
 all: \
   .lib.done.log
 	$(MAKE) \
@@ -44,9 +46,31 @@ all: \
 	  --directory lib
 	touch $@
 
+# The two CASE-Utility... files are to trigger rebuilds based on command-line interface changes or version increments.
+.venv.done.log: \
+  dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/case_shacl_inheritance_reviewer/__init__.py \
+  dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/setup.cfg \
+  requirements.txt
+	rm -rf venv
+	$(PYTHON3) -m venv \
+	  venv
+	source venv/bin/activate \
+	  && pip install \
+	    --upgrade \
+	    pip \
+	    setuptools \
+	    wheel
+	source venv/bin/activate \
+	  && pip install \
+	    dependencies/CASE-Utility-SHACL-Inheritance-Reviewer
+	source venv/bin/activate \
+	  && pip install \
+	    --requirement requirements.txt
+	touch $@
+
 check: \
-  .git_submodule_init.done.log \
-  .lib.done.log
+  .lib.done.log \
+  .venv.done.log
 	$(MAKE) \
 	  --directory ontology \
 	  check
@@ -59,7 +83,10 @@ clean: \
   clean-ontology
 	@rm -f \
 	  .git_submodule_init.done.log \
-	  .lib.done.log
+	  .lib.done.log \
+	  .venv.done.log
+	@rm -rf \
+	  venv
 
 clean-ontology:
 	@$(MAKE) \
@@ -70,3 +97,15 @@ clean-tests:
 	@$(MAKE) \
 	  --directory tests \
 	  clean
+
+# Maintain timestamp order.
+dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/case_shacl_inheritance_reviewer/__init__.py: \
+  .git_submodule_init.done.log
+	touch -c $@
+	test -r $@
+
+# Maintain timestamp order.
+dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/setup.cfg: \
+  .git_submodule_init.done.log
+	touch -c $@
+	test -r $@

ontology/uco/master/Makefile

@@ -18,12 +18,11 @@ top_srcdir := $(shell cd ../../.. ; pwd)
 all: \
   catalog-v001.xml
 
-# TODO - Move virtual environment creation up to root directory and re-order top_srcdir's descent.
 catalog-v001.xml: \
   $(top_srcdir)/src/create-catalog-v001.xml.py \
-  $(top_srcdir)/tests/.venv.done.log
+  $(top_srcdir)/.venv.done.log
 	rm -f _$@
-	source $(top_srcdir)/tests/venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && python3 $(top_srcdir)/src/create-catalog-v001.xml.py \
 	    _$@ \
 	    domain_directories.tsv \

tests/.gitignore

@@ -1,6 +1,3 @@
 .shapes.done.log
-.venv.done.log
-_*
 inheritance_review.ttl
 uco_monolithic.ttl
-venv

tests/Makefile

@@ -15,8 +15,6 @@ SHELL := /bin/bash
 
 top_srcdir := $(shell cd .. ; pwd)
 
-PYTHON3 ?= $(shell which python3.9 2>/dev/null || which python3.8 2>/dev/null || which python3.7 2>/dev/null || which python3.6 2>/dev/null || which python3)
-
 uco_turtle_files := $(shell /bin/ls $(top_srcdir)/ontology/*/*.ttl $(top_srcdir)/ontology/*/*/*.ttl)
 
 imported_ontology_files := \
@@ -31,42 +29,19 @@ all:
 # Ensure the UCO-internal shapes pass their own tests.
 .shapes.done.log: \
   $(top_srcdir)/ontology/owl/owl.ttl \
-  .venv.done.log \
+  $(top_srcdir)/.venv.done.log \
   shapes/uco-closure-qc.ttl \
   shapes/uco-qc.ttl
 	$(MAKE) \
 	  --directory shapes \
 	  check
 	touch $@
 
-# The two CASE-Utility... files are to trigger rebuilds based on command-line interface changes or version increments.
-.venv.done.log: \
-  $(top_srcdir)/.git_submodule_init.done.log \
-  $(top_srcdir)/dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/case_shacl_inheritance_reviewer/__init__.py \
-  $(top_srcdir)/dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/setup.cfg \
-  requirements.txt
-	rm -rf venv
-	$(PYTHON3) -m venv \
-	  venv
-	source venv/bin/activate \
-	  && pip install \
-	    --upgrade \
-	    pip \
-	    setuptools \
-	    wheel
-	source venv/bin/activate \
-	  && pip install \
-	    $(top_srcdir)/dependencies/CASE-Utility-SHACL-Inheritance-Reviewer
-	source venv/bin/activate \
-	  && pip install \
-	    --requirement requirements.txt
-	touch $@
-
 check: \
   check-dependencies \
   inheritance_review.ttl \
   uco_monolithic.ttl
-	source venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pytest \
 	    --ignore examples \
 	    --ignore shapes \
@@ -76,7 +51,7 @@ check: \
 	  check
 
 check-dependencies: \
-  .venv.done.log
+  $(top_srcdir)/.venv.done.log
 	$(MAKE) \
 	  --directory dependencies \
 	  check
@@ -91,14 +66,12 @@ clean:
 	@rm -f \
 	  .*.done.log \
 	  uco_monolithic.ttl
-	@rm -rf \
-	  venv
 
 inheritance_review.ttl: \
   $(uco_turtle_files) \
-  .venv.done.log
+  $(top_srcdir)/.venv.done.log
 	rm -f _$@
-	source venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && case_shacl_inheritance_reviewer \
 	    --strict \
 	    _$@ \
@@ -112,19 +85,19 @@ uco_monolithic.ttl: \
   $(uco_turtle_files) \
   .shapes.done.log \
   thing.ttl
-	source venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
           && rdfpipe \
 	    --input-format ttl \
 	    --output-format ttl \
 	    $(uco_turtle_files) \
 	    > __$@
 	# Review UCO closure for versioning consistency.
-	source venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
           && rdfpipe \
 	  __$@ \
 	  $(imported_ontology_files) \
 	  > ___$@
-	source venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pyshacl \
 	    --data-file-format turtle \
 	    --format turtle \
@@ -133,7 +106,7 @@ uco_monolithic.ttl: \
 	    --shacl-file-format turtle \
 	    ___$@
 	# Review UCO closure with SHACL-SHACL.
-	source venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pyshacl \
 	    --data-file-format turtle \
 	    --format turtle \
@@ -145,7 +118,7 @@ uco_monolithic.ttl: \
 	# Closure tests have passed; remove closure file.
 	rm ___$@
 	# Review UCO for practice conformance.
-	source venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pyshacl \
 	    --data-file-format turtle \
 	    --format turtle \
@@ -154,7 +127,7 @@ uco_monolithic.ttl: \
 	    --shacl-file-format turtle \
 	    __$@
 	# Review UCO for OWL 2 DL conformance.
-	source venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pyshacl \
 	    --data-file-format turtle \
 	    --format turtle \

tests/dependencies/Makefile

@@ -15,8 +15,6 @@ SHELL := /bin/bash
 
 top_srcdir := $(shell cd ../.. ; pwd)
 
-tests_srcdir := $(top_srcdir)/tests
-
 all:
 
 check: \
@@ -29,10 +27,10 @@ clean:
 
 uco-owl-co.done.log: \
   $(top_srcdir)/dependencies/collections-ontology/collections.owl \
-  $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/.venv.done.log \
   $(top_srcdir)/ontology/owl/owl.ttl
 	# Review for OWL 2 DL conformance.
-	source $(tests_srcdir)/venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pyshacl \
 	    --data-file-format xml \
 	    --format turtle \
@@ -45,10 +43,10 @@ uco-owl-co.done.log: \
 
 uco-owl-error.done.log: \
   $(top_srcdir)/dependencies/error/docs/current/error.ttl \
-  $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/.venv.done.log \
   $(top_srcdir)/ontology/owl/owl.ttl
 	# Review for OWL 2 DL conformance.
-	source $(tests_srcdir)/venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pyshacl \
 	    --data-file-format turtle \
 	    --format turtle \

tests/examples/Makefile

@@ -62,9 +62,9 @@ all: \
 # characteristics.
 %_validation.ttl: \
   %.json \
-  $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/.venv.done.log \
   $(tests_srcdir)/uco_monolithic.ttl
-	source $(tests_srcdir)/venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pyshacl \
 	    --allow-warnings \
 	    --data-file-format json-ld \
@@ -116,7 +116,7 @@ check: \
   thread_PASS_validation.ttl \
   thread_XFAIL_validation.ttl \
   uco_thing_XFAIL_validation.ttl
-	source $(tests_srcdir)/venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pytest \
 	    --log-level=DEBUG
 

tests/shapes/Makefile

@@ -15,8 +15,6 @@ SHELL := /bin/bash
 
 top_srcdir := $(shell cd ../.. ; pwd)
 
-tests_srcdir := $(top_srcdir)/tests
-
 all: \
   qc_monolithic.ttl
 	$(MAKE) \
@@ -51,7 +49,7 @@ check: \
 	$(MAKE) \
 	  --directory examples_uco_qc \
 	  check
-	source $(tests_srcdir)/venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pytest \
 	    --log-level=DEBUG \
 	    --verbose \
@@ -77,12 +75,12 @@ clean:
 	  qc_monolithic.ttl
 
 qc_monolithic.ttl: \
-  $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/.venv.done.log \
   $(top_srcdir)/.lib.done.log \
   uco-closure-qc.ttl \
   uco-qc.ttl
 	rm -f __$@ _$@
-	source $(tests_srcdir)/venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && rdfpipe \
 	    --output-format turtle \
 	    uco-closure-qc.ttl \

tests/shapes/examples_uco_owl/Makefile

@@ -15,9 +15,7 @@ SHELL := /bin/bash
 
 top_srcdir := $(shell cd ../../.. ; pwd)
 
-tests_srcdir := $(top_srcdir)/tests
-
-shapes_srcdir := $(tests_srcdir)/shapes
+shapes_srcdir := $(top_srcdir)/tests/shapes
 
 sample_ttls := $(wildcard *_PASS.ttl *_XFAIL.ttl)
 
@@ -37,10 +35,10 @@ all: \
 # characteristics.
 %_validation.ttl: \
   %.ttl \
-  $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/.venv.done.log \
   $(top_srcdir)/ontology/owl/owl.ttl
 	rm -f __$@ _$@
-	source $(tests_srcdir)/venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pyshacl \
 	    --allow-warnings \
 	    --data-file-format turtle \

tests/shapes/examples_uco_qc/Makefile

@@ -15,9 +15,7 @@ SHELL := /bin/bash
 
 top_srcdir := $(shell cd ../../.. ; pwd)
 
-tests_srcdir := $(top_srcdir)/tests
-
-shapes_srcdir := $(tests_srcdir)/shapes
+shapes_srcdir := $(top_srcdir)/tests/shapes
 
 sample_ttls := $(wildcard *_PASS.ttl *_XFAIL.ttl)
 
@@ -37,10 +35,10 @@ all: \
 # characteristics.
 %_validation.ttl: \
   %.ttl \
-  $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/.venv.done.log \
   $(shapes_srcdir)/qc_monolithic.ttl
 	rm -f __$@ _$@
-	source $(tests_srcdir)/venv/bin/activate \
+	source $(top_srcdir)/venv/bin/activate \
 	  && pyshacl \
 	    --allow-warnings \
 	    --data-file-format turtle \