make targets to copy specs and test data, centralize test data

.github/workflows/py-unittest.yaml

@@ -26,6 +26,11 @@ jobs:
         python-version: [ '3.8' ]
     steps:
       - uses: actions/checkout@v2
+
+      - name: Check test data matches the global test data files
+        run: diff -rc tests/data ../../tests/data
+        shell: bash
+
       - name: Set up Python
         uses: actions/setup-python@v2
         with:

.github/workflows/r-check.yaml

@@ -26,6 +26,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
+      - name: Check test data matches the global test data files
+        run: diff -rc tests/data-tests ../../tests/data
+        shell: bash
+
       - name: Install dependencies
         run: |
           install.packages(c("remotes", "testthat", "roxygen2", "devtools", "rcmdcheck"))

Makefile

@@ -0,0 +1,55 @@
+# helper commands for keeping the language directories in sync
+
+# note: "help" MUST be the first target in the file,
+# when the user types "make" they should get help info
+help:
+	@echo ""
+	@echo "Helper commands for AIRR Standards repository"
+	@echo ""
+	@echo "make gen-v2       -- Generate OpenAPI V2 spec from the V3 spec"
+	@echo "make build-docs   -- Build documentation"
+	@echo "make spec-copy    -- Copy spec files to language directories"
+	@echo "make data-copy    -- Copy test data files to language directories"
+	@echo "make checks       -- Run consistency checks on spec files"
+	@echo "make tests        -- Run all language test suites"
+	@echo "make python-tests -- Run Python test suite"
+	@echo "make r-tests      -- Run R test suite"
+	@echo "make js-tests     -- Run Javascript test suite"
+	@echo ""
+
+gen-v2:
+	@echo "Not implemented"
+
+build-docs:
+	sphinx-build -a -E -b html docs docs/_build/html
+
+spec-copy:
+	@echo "Copying specs to language directories"
+	cp specs/airr-schema.yaml lang/python/airr/specs
+	cp specs/airr-schema-openapi3.yaml lang/python/airr/specs
+	cp specs/airr-schema.yaml lang/R/inst/extdata
+	cp specs/airr-schema-openapi3.yaml lang/R/inst/extdata
+#	cp specs/airr-schema.yaml lang/js/
+#	cp specs/airr-schema-openapi3.yaml lang/js/
+
+data-copy:
+	@echo "Copying test data to language directories"
+	cp tests/data/* lang/python/tests/data
+	cp tests/data/* lang/R/tests/data-tests
+
+checks:
+	@echo "Running consistency checks on spec files"
+	python3 tests/check-consistency-formats.py
+
+tests: python-tests r-tests js-tests
+
+python-tests:
+	@echo "Running Python test suite"
+	cd lang/python; python3 -m unittest discover
+
+r-tests:
+	@echo "Running R test suite"
+	cd lang/R; R -e "library(devtools); test()"
+
+js-tests:
+	@echo "Running Javascript test suite"