add an optional test to make sure full validate produce is run when l…

.github/workflows/make-tests.yaml

@@ -27,4 +27,5 @@ jobs:
           pip install .
           pip install pytest
       - name: run make on rules
+        # reminder: please run `make travis_test_full` locally to include slow running tests not suitable for CI
         run: make travis_test

Makefile

@@ -8,22 +8,47 @@ PACKAGES = ontobio prefixcommons
 subpackage_tests: $(patsubst %,test-%,$(PACKAGES))
 
 test:
-	pytest tests/*.py tests/unit/
+	pytest -m "not slow" tests/*.py tests/unit/
 
 debug_test:
-	pytest -s -vvvv tests/*.py
+	pytest -m "not slow" -s -vvvv tests/*.py
 
 t-%:
-	pytest tests/test_$*.py
+	pytest -m "not slow" tests/test_$*.py
 
 tv-%:
-	pytest -s tests/test_$*.py
+	pytest -m "not slow" -s tests/test_$*.py
 
 foo:
 	which pytest
 
 # only run local tests
 travis_test:
+	@if [ -d ".venv" ] && [ -f "pyproject.toml" ]; then \
+		echo "Running tests in Poetry environment..."; \
+		poetry run pytest -m "not slow" tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \
+		tests/test_rdfgen.py tests/test_phenosim_engine.py tests/test_ontol.py \
+		tests/test_validation_rules.py tests/unit/test_annotation_scorer.py \
+		tests/test_goassociation_model.py tests/test_relations.py \
+		tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \
+		tests/test_collections.py \
+		tests/test_gocamgen.py \
+		tests/test_gpi_isoform_replacement.py \
+		tests/test_validate_cli.py; \
+	else \
+		pytest -m "not slow" tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \
+		tests/test_rdfgen.py tests/test_phenosim_engine.py tests/test_ontol.py \
+		tests/test_validation_rules.py tests/unit/test_annotation_scorer.py \
+		tests/test_goassociation_model.py tests/test_relations.py \
+		tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \
+		tests/test_collections.py \
+		tests/test_gocamgen.py \
+		tests/test_gpi_isoform_replacement.py \
+		tests/test_validate_cli.py; \
+	fi
+
+
+travis_test_full:
 	@if [ -d ".venv" ] && [ -f "pyproject.toml" ]; then \
 		echo "Running tests in Poetry environment..."; \
 		poetry run pytest tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \
@@ -33,7 +58,8 @@ travis_test:
 		tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \
 		tests/test_collections.py \
 		tests/test_gocamgen.py \
-		tests/test_gpi_isoform_replacement.py; \
+		tests/test_gpi_isoform_replacement.py \
+		tests/test_validate_cli.py; \
 	else \
 		pytest tests/test_*local*.py tests/test_*parse*.py tests/test*writer*.py tests/test_qc.py \
 		tests/test_rdfgen.py tests/test_phenosim_engine.py tests/test_ontol.py \
@@ -42,9 +68,11 @@ travis_test:
 		tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \
 		tests/test_collections.py \
 		tests/test_gocamgen.py \
-		tests/test_gpi_isoform_replacement.py; \
+		tests/test_gpi_isoform_replacement.py \
+		tests/test_validate_cli.py; \
 	fi
 
+
 cleandist:
 	rm dist/* || true
 

bin/README.md

@@ -1,16 +1,26 @@
 See [command line docs](http://ontobio.readthedocs.io/en/latest/commandline.html#commandline) on ReadTheDocs
 
 To test validate.py "validate" command, the command that produces the final GPADs in the pipeline via the "mega make" 
-(aka: "produces GAFs, GPADs, ttl" stage), on a particular source:
+(aka: "produces GAFs, GPADs, ttl" stage), on a particular source, run:
+```bash
+make test_travis_full
+```
+
+This makefile target will run the full validate.produce command using goa_cow, mgi, zfin, and goa_chicken sources,
+producing GPAD, GAF files in the groups subdirectory and then do a check of the content of these products.  These
+tests only run manually, not via CI because they take minutes to run.
 
+alternatively, you can run the following commands to test the validate.produce command on a particular source, locally:
+
+```bash
 Note: snapshot below in the URL can be changed to any pipeline branch; its listed here for ease of cp/paste.
 ```bash
 poetry install
 poetry run validate produce -m ../go-site/metadata --gpad -t . -o go-basic.json --base-download-url "http://skyhook.berkeleybop.org/snapshot/" --only-dataset mgi MGI --gpad-gpi-output-version 2.0
 poetry run validate produce -m ../go-site/metadata --gpad -t . -o go-basic.json --base-download-url "http://skyhook.berkeleybop.org/snapshot/" --only-dataset goa_chicken goa --gpad-gpi-output-version 2.0
+poetry run validate produce -m ../go-site/metadata --gpad -t . -o go-basic.json --base-download-url "http://skyhook.berkeleybop.org/snapshot/" --only-dataset zfin ZFIN --gpad-gpi-output-version 2.0
 ```
 
-
 To test whether a GAF file is valid (passes all the GORules):
 ```bash
 poetry install

fixed_test.gaf

@@ -2,7 +2,7 @@
 !
 !generated-by: GOC
 !
-!date-generated: 2024-07-29T15:02
+!date-generated: 2024-08-12T14:15
 !
 !Header from source association file:
 !=================================

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')