Makefile

# Makefile for Python project

.DELETE_ON_ERROR:
.PHONY: FORCE
.PRECIOUS :
.SUFFIXES:

SHELL:=/bin/bash -e -o pipefail
SELF:=$(firstword $(MAKEFILE_LIST))

PKG=hgvs
PKGD=$(subst .,/,${PKG})
PYV:=3.9
VEDIR=venv/${PYV}

TEST_DIRS:=tests
DOC_TESTS:=docs hgvs ./README.rst


############################################################################
#= BASIC USAGE
default: help

#=> help -- display this help message
help:
	@sbin/makefile-extract-documentation "${SELF}"


############################################################################
#= SETUP, INSTALLATION, PACKAGING

#=> venv: make a Python 3 virtual environment
venv: ${VEDIR}
venv/%:
	python$* -mvenv $@; \
	source $@/bin/activate; \
	python -m ensurepip --upgrade; \
	pip install --upgrade pip setuptools

#=> setup: setup/upgrade packages *in current environment*
.PHONY: setup
setup: etc/develop.reqs etc/install.reqs
	if [ -s $(word 1,$^) ]; then pip install --upgrade -r $(word 1,$^); fi
	if [ -s $(word 2,$^) ]; then pip install --upgrade -r $(word 2,$^); fi

#=> devready: create venv, install prerequisites, install pkg in develop mode
.PHONY: devready
devready:
	make ${VEDIR} && source ${VEDIR}/bin/activate && make setup develop
	@echo '#################################################################################'
	@echo '###  Do not forget to `source ${VEDIR}/bin/activate` to use this environment  ###'
	@echo '#################################################################################'

#=> develop: install package in develop mode
#=> install: install package
#=> bdist bdist_egg bdist_wheel build sdist: distribution options
.PHONY: bdist bdist_egg bdist_wheel build build_sphinx sdist install develop
develop:
	pip install -e .
bdist bdist_egg bdist_wheel build sdist install: %:
	python setup.py $@




############################################################################
#= TESTING
# see test configuration in setup.cfg


#=> test: execute tests
#=> test-code: test code (including embedded doctests)
#=> test-docs: test example code in docs
#=> test-/tag/ -- run tests marked with /tag/
# TODO: rationalize tags
# find tests -name \*.py | xargs perl -ln0e 'while (m/@pytest.mark.(\w+)/g) {print $1 if not $seen{$1}++}'  | sort
# => extra fx issues mapping models normalization parametrize pnd quick regression validation
.PHONY: test test-code test-docs
test:
	python setup.py pytest
test-code:
	python setup.py pytest --addopts="${TEST_DIRS}"
test-docs:
	python setup.py pytest --addopts="${DOC_TESTS}"
test-%:
	python setup.py pytest --addopts="-m '$*' ${TEST_DIRS}"

#=> tox -- run all tox tests
tox:
	tox


############################################################################
#= UTILITY TARGETS

# N.B. Although code is stored in github, I use hg and hg-git on the command line
#=> reformat: reformat code with yapf and commit
.PHONY: reformat
reformat:
	@if hg sum | grep -qL '^commit:.*modified'; then echo "Repository not clean" 1>&2; exit 1; fi
	@if hg sum | grep -qL ' applied'; then echo "Repository has applied patches" 1>&2; exit 1; fi
	yapf -i -r "${PKGD}" tests
	hg commit -m "reformatted with yapf"

#=> docs -- make sphinx docs
.PHONY: docs
docs: develop
	# RTD makes json. Build here to ensure that it works.
	make -C docs html json

############################################################################
#= CLEANUP

#=> clean: remove temporary and backup files
.PHONY: clean
clean:
	find . \( -name \*~ -o -name \*.bak \) -print0 | xargs -0r rm
	-make -C docs $@
	-make -C examples $@

#=> cleaner: remove files and directories that are easily rebuilt
.PHONY: cleaner
cleaner: clean
	rm -fr .cache *.egg-info build dist docs/_build htmlcov
	find . \( -name \*.pyc -o -name \*.orig -o -name \*.rej \) -print0 | xargs -0r rm
	find . -name __pycache__ -print0 | xargs -0r rm -fr
	/bin/rm -fr examples/.ipynb_checkpoints
	/bin/rm -f hgvs.{dot,svg,png,sfood}
	-make -C docs $@
	-make -C examples $@

#=> cleanest: remove files and directories that require more time/network fetches to rebuild
.PHONY: cleanest
cleanest: cleaner
	rm -fr .eggs .tox venv
	-make -C docs $@
	-make -C examples $@


############################################################################
#= HGVS specific

#=> code-check -- check code with flake8
code-check:
	flake8 hgvs test --output-file=$@.txt

#=> docs-aux -- make generated docs for sphinx
docs-aux:
	make -C misc/railroad docs-install
	make -C examples docs-install

#=> hgvs.svg -- import graph; requires snakefood
hgvs.sfood:
	sfood hgvs >"$@.tmp"
	/bin/mv "$@.tmp" "$@"
hgvs.dot: hgvs.sfood
	sfood-graph -p <$< >"$@.tmp"
	/bin/mv "$@.tmp" "$@"
hgvs.svg: hgvs.dot
	dot -Tsvg <$< >"$@.tmp"
	/bin/mv "$@.tmp" "$@"


# <LICENSE>
# Copyright 2018 HGVS Contributors (https://github.com/biocommons/hgvs)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# </LICENSE>