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Makefile
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# system python interpreter. used only to create virtual environment
PY = python3
VENV = venv
BIN=$(VENV)/bin
.PHONY: all
all: install test
$(VENV):
$(PY) -m venv $(VENV)
$(BIN)/pip install --upgrade wheel gdown build pytest flake8 pip
touch $(VENV)
external/lipidlynxx/README.md:
git submodule update --init --recursive
build/lipidlynxx: external/lipidlynxx/README.md
mkdir -p build
cp -r external/lipidlynxx build/
build/lipidlynxx/pyproject.toml: build/lipidlynxx
./scripts/lipidlynxx_setuptools.sh build/lipidlynxx
data/alex123/alex123_db.h5: $(VENV)
mkdir -p data/alex123
$(BIN)/gdown 1PCyaofEvpOkysWM_zMUPjU-xIJSPzQVH -O data/alex123/alex123_db.h5
data/lion/lion_ontology_graph.obo: $(VENV)
mkdir -p data/lion
$(BIN)/gdown 1W5x38nUKKAv12N7f8RTqZ09hpSaLz8Cv -O data/lion/lion_ontology_graph.obo
data/lion/lion_association_table.tsv: $(VENV)
mkdir -p data/lion
$(BIN)/gdown 1bhdBM3LgBH9W74zn9seJeup-H9FFG7RN -O data/lion/lion_association_table.tsv
src/lipidlibrarian/data: data/alex123/alex123_db.h5 data/lion/lion_ontology_graph.obo data/lion/lion_association_table.tsv
mkdir -p src/lipidlibrarian/data
mkdir -p src/lipidlibrarian/data/alex123
mkdir -p src/lipidlibrarian/data/linex
mkdir -p src/lipidlibrarian/data/lion
cp data/adducts.csv src/lipidlibrarian/data/
cp data/alex123/alex123_db.h5 src/lipidlibrarian/data/alex123/
cp data/linex/linex_data.pbz2 src/lipidlibrarian/data/linex/
cp data/lion/lion_ontology_graph.obo src/lipidlibrarian/data/lion/
cp data/lion/lion_association_table.tsv src/lipidlibrarian/data/lion/
.PHONY: build
build: $(VENV) pyproject.toml src/lipidlibrarian/data
$(BIN)/python3 -m build
.PHONY: install
install: $(VENV) src/lipidlibrarian/data
$(BIN)/pip install .
.PHONY: install_optional
install_optional: $(VENV) build/lipidlynxx/pyproject.toml
$(BIN)/pip install build/lipidlynxx
.PHONY: lint
lint: $(VENV)
$(BIN)/flake8 --ignore=E501 src
.PHONY: test
test: install
$(BIN)/pytest test
.PHONY: clean
clean:
rm -rf build
rm -rf dist
rm -rf lipidlibrarian.egg-info
rm -rf src/lipidlibrarian.egg-info
rm -rf src/lipidlibrarian/data
rm -rf /tmp/lipidlynxx
rm -rf $(VENV)
find . -type f -name *.pyc -delete
find . -type d -name __pycache__ -delete