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Makefile
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#* Variables
SHELL := /usr/bin/env bash
PYTHON := python
PYTHONPATH := `pwd`
#* Docker variables
IMAGE := score
VERSION := latest
#* Poetry
.PHONY: poetry-download
poetry-download:
curl -sSL https://install.python-poetry.org | $(PYTHON) -
.PHONY: poetry-remove
poetry-remove:
curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | $(PYTHON) - --uninstall
#* Installation
.PHONY: install
install:
poetry lock -n && poetry export --without-hashes > requirements.txt
poetry install -n
-poetry run mypy --install-types --non-interactive ./
.PHONY: pre-commit-install
pre-commit-install:
poetry run pre-commit install
#* Formatters
.PHONY: codestyle
codestyle:
poetry run pyupgrade --exit-zero-even-if-changed --py37-plus **/*.py
poetry run isort --settings-path pyproject.toml ./
poetry run black --config pyproject.toml ./
.PHONY: formatting
formatting: codestyle
#* Linting
.PHONY: test
test:
rm -f -r tests/test_example/schictools_data/
rm -f -r tests/test_example/schic-topic-model/
rm -f -r tests/test_example/data/higashi_data/
rm -f -r tests/test_example/data/inadequate_cells/
rm -f -r tests/test_example/data/sparse_matrices/
rm -f -r tests/test_example/threeDVI/
rm -f -r tests/test_example/vade/
rm -f -r tests/test_example/data/toki_data
rm -f -r tests/test_example/data/read_info
rm -f -r tests/test_example/data/inadequate_cells
PYTHONPATH=$(PYTHONPATH) poetry run pytest -c pyproject.toml --cov-report=html --cov=score tests/
poetry run coverage-badge -o assets/images/coverage.svg -f
.PHONY: profile
profile:
rm -f -r tests/test_example/schictools_data/
rm -f -r tests/test_example/schic-topic-model/
rm -f -r tests/test_example/data/higashi_data/
rm -f -r tests/test_example/data/inadequate_cells/
rm -f -r tests/test_example/data/sparse_matrices/
rm -f -r tests/test_example/threeDVI/
rm -f -r tests/test_example/vade/
rm -f -r tests/test_example/data/toki_data
rm -f -r tests/test_example/data/read_info
rm -f -r tests/test_example/data/inadequate_cells
python -m cProfile -o profile -m pytest -c pyproject.toml --cov-report=html --cov=score tests/
python score/display_profile.py
.PHONY: check-codestyle
# check-codestyle:
# poetry run isort --diff --check-only --settings-path pyproject.toml ./
# poetry run black --diff --check --config pyproject.toml ./
# poetry run darglint --verbosity 2 score tests
.PHONY: mypy
mypy:
poetry run mypy --config-file pyproject.toml ./
.PHONY: check-safety
check-safety:
poetry check
#poetry run safety check --full-report
#poetry run bandit -ll --recursive score tests
.PHONY: lint
lint: test mypy check-safety
.PHONY: update-dev-deps
update-dev-deps:
poetry add -D bandit@latest darglint@latest "isort[colors]@latest" mypy@latest pre-commit@latest pydocstyle@latest pylint@latest pytest@latest pyupgrade@latest safety@latest coverage@latest coverage-badge@latest pytest-html@latest pytest-cov@latest
poetry add -D --allow-prereleases black@latest
#* Docker
# Example: make docker-build VERSION=latest
# Example: make docker-build IMAGE=some_name VERSION=0.1.0
.PHONY: docker-build
docker-build:
@echo Building docker $(IMAGE):$(VERSION) ...
docker build \
-t $(IMAGE):$(VERSION) . \
-f ./docker/Dockerfile --no-cache
# Example: make docker-remove VERSION=latest
# Example: make docker-remove IMAGE=some_name VERSION=0.1.0
.PHONY: docker-remove
docker-remove:
@echo Removing docker $(IMAGE):$(VERSION) ...
docker rmi -f $(IMAGE):$(VERSION)
#* Cleaning
.PHONY: pycache-remove
pycache-remove:
find . | grep -E "(__pycache__|\.pyc|\.pyo$$)" | xargs rm -rf
.PHONY: dsstore-remove
dsstore-remove:
find . | grep -E ".DS_Store" | xargs rm -rf
.PHONY: mypycache-remove
mypycache-remove:
find . | grep -E ".mypy_cache" | xargs rm -rf
.PHONY: ipynbcheckpoints-remove
ipynbcheckpoints-remove:
find . | grep -E ".ipynb_checkpoints" | xargs rm -rf
.PHONY: pytestcache-remove
pytestcache-remove:
find . | grep -E ".pytest_cache" | xargs rm -rf
.PHONY: build-remove
build-remove:
rm -rf build/
.PHONY: cleanup
cleanup: pycache-remove dsstore-remove mypycache-remove ipynbcheckpoints-remove pytestcache-remove