.PHONY: run lint test test-cov

run:

replay provenance \

--i-in-fp provenance_lib/tests/data/v5_uu_emperor.qzv \

--p-use-recorded-metadata \

--p-verbose \

--o-metadata-out-fp './gerbils-time' \

--o-out-fp ./replay_scripts/sample_replay.sh

run-py:

replay provenance \

--i-in-fp provenance_lib/tests/data/v5_uu_emperor.qzv \

--p-usage-driver python3 \

--p-use-recorded-metadata \

--p-verbose \

--o-metadata-out-fp './gerbils-time' \

--o-out-fp ./replay_scripts/sample_replay.py

run-cite:

replay citations \

--i-in-fp provenance_lib/tests/data/v5_uu_emperor.qzv \

--p-verbose \

--o-out-fp ./replay_scripts/sample-citations.bib

cite-everything:

replay citations \

--i-in-fp ~/data/alzmice/ileum \

--p-recurse \

--p-verbose \

--o-out-fp ./replay_scripts/every-citation-2.bib

repro-supp:

replay supplement \

--i-in-fp provenance_lib/tests/data/v5_uu_emperor.qzv \

--o-out-fp ./replay_scripts/supplement.zip

# TODO: install and dev targets

# Conda recipe will use make install and will copy the tab-complete language

# https://github.com/qiime2/q2cli/blob/master/hooks/50_activate_q2cli_tab_completion.sh

# from /bin or /scripts over to activate.d

# https://github.com/qiime2/q2cli/blob/ab0afe7917977c1272cad2d334607f7e6b1f6e41/ci/recipe/meta.yaml#L12

# NOTE: Dev will also need to install testing deps, and mypy should prob. move

# over to extras. These are all referenced by the [dev] key in extras

# dev:

# pip install -e .[dev]

lint:

flake8

test: lint

py.test

test-cov: lint

pytest --cov-report=term-missing --cov=provenance_lib

mypy:

mypy -p provenance_lib

uml:

# pyreverse is packaged with pylint, and installable with `pip install pylint`

pyreverse -ASmy -k -o puml provenance_lib/ --ignore tests -p packages

uml-full:

pyreverse -ASmy --colorized -o puml provenance_lib/ --ignore tests -p classes

uml-archive-parser:

pyreverse -ASmy --colorized -o puml provenance_lib/_archive_parser.py

dev:

pip install -e .

clean:

rm -r recorded_metadata replay_scripts

install:

python setup.py install