diff clipkit_repo/Makefile @ 2:e9cf321ee7be draft

"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clipkit_repo/Makefile	Fri Mar 25 17:33:41 2022 +0000
@@ -0,0 +1,43 @@
+profile:
+	python3 -m cProfile -s 'time' clipkit-runner.py  tests/integration/samples/EOG092C0CZK_aa_aln.fasta -o output/test > output/large_profile.txt
+
+run:
+	python3 -m clipkit-runner tests/integration/samples/12_YIL115C_Anc_2.253_aa_aln.fasta -o output/test --log
+
+run.simple:
+	python3 -m clipkit-runner tests/integration/samples/simple.fa -o output/simple --log	
+
+install:
+	# install so clipkit command is available in terminal
+	python setup.py install
+
+develop:
+	# https://setuptools.readthedocs.io/en/latest/setuptools.html#development-mode
+	python setup.py develop
+
+test: test.unit test.integration
+
+test.unit:
+	python -m pytest -m "not integration"
+
+test.integration:
+	rm -rf output/
+	mkdir output/
+	python -m pytest --basetemp=output -m "integration"
+
+test.fast:
+	python -m pytest -m "not (integration or slow)"
+	rm -rf output/
+	mkdir output/
+	python -m pytest --basetemp=output -m "integration and not slow"
+
+# used by GitHub actions during CI workflow
+test.coverage: coverage.unit coverage.integration
+
+coverage.unit:
+	python -m pytest --cov=./ -m "not integration" --cov-report=xml:unit.coverage.xml
+
+coverage.integration:
+	rm -rf output/
+	mkdir output/
+	python -m pytest --basetemp=output --cov=./ -m "integration" --cov-report=xml:integration.coverage.xml