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Makefile
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DOCKER_COMPOSE_DEV = docker-compose
DOCKER_COMPOSE_CI = docker-compose -f docker-compose.yml -f docker-compose.ci.yml
DOCKER_COMPOSE = $(DOCKER_COMPOSE_DEV)
VENV = venv
PIP = $(VENV)/bin/pip
PYTHON = $(VENV)/bin/python
USER_ID = $(shell id -u)
GROUP_ID = $(shell id -g)
DATA_SCIENCE_DAGS_PROJECTS_HOME = $(shell dirname $(shell pwd))
DATA_SCIENCE_DAGS_JUPYTER_PORT = $(shell bash -c 'source .env && echo $$DATA_SCIENCE_DAGS_JUPYTER_PORT')
DATA_SCIENCE_DAGS_PEERSCOUT_API_PORT = $(shell bash -c 'source .env && echo $$DATA_SCIENCE_DAGS_PEERSCOUT_API_PORT')
JUPYTER_DOCKER_COMPOSE = USER_ID="$(USER_ID)" GROUP_ID="$(GROUP_ID)" \
DATA_SCIENCE_DAGS_JUPYTER_PORT="$(DATA_SCIENCE_DAGS_JUPYTER_PORT)" \
DATA_SCIENCE_DAGS_PROJECTS_HOME="$(DATA_SCIENCE_DAGS_PROJECTS_HOME)" \
$(DOCKER_COMPOSE)
JUPYTER_RUN = $(JUPYTER_DOCKER_COMPOSE) run --rm jupyter
PEERSCOUT_API_DOCKER_COMPOSE = DATA_SCIENCE_DAGS_PEERSCOUT_API_PORT="$(DATA_SCIENCE_DAGS_PEERSCOUT_API_PORT)" \
$(DOCKER_COMPOSE)
PEERSCOUT_API_DEV_DOCKER_PYTHON = $(PEERSCOUT_API_DOCKER_COMPOSE) run --rm peerscout-api-dev python
PROJECT_FOLDER = /home/jovyan/data-science-dags
DEV_RUN = $(JUPYTER_DOCKER_COMPOSE) run --rm data-science-pipelines-dev
# Cells starts scrolling horizontally after 116 characters
NOTEBOOK_MAX_LINE_LENGTH = 116
NOTEBOOK_PYLINT_EXCLUSIONS = pointless-statement,expression-not-assigned,trailing-newlines,wrong-import-position,redefined-outer-name
OUTPUT_DATASET = data_science
MAX_MANUSCRIPTS = 10
MAX_EDITORS = 10
ARGS =
.PHONY: build
PYTEST_WATCH_MODULES = tests/unit_test
venv-clean:
@if [ -d "$(VENV)" ]; then \
rm -rf "$(VENV)"; \
fi
venv-create:
python3 -m venv $(VENV)
dev-install:
$(PIP) install --disable-pip-version-check -r requirements.build.txt
$(PIP) install --disable-pip-version-check \
-r requirements.dev.txt \
-r requirements.jupyter.txt \
-r requirements.pipelines.txt \
-r requirements.prophet.txt \
-r requirements.api.txt
$(PIP) install --disable-pip-version-check -e . --no-deps
dev-venv: venv-create dev-install
dev-flake8:
$(PYTHON) -m flake8 data_science_pipeline peerscout_api tests tests_peerscout_api setup.py
dev-pylint:
$(PYTHON) -m pylint data_science_pipeline peerscout_api tests tests_peerscout_api setup.py
dev-mypy:
$(PYTHON) -m mypy data_science_pipeline peerscout_api tests tests_peerscout_api setup.py
dev-notebook-lint:
$(VENV)/bin/jupyter nbconvert \
--to=script \
--output-dir=.temp/converted-notebooks/ \
./notebooks/**/*.ipynb
$(PYTHON) -m pylint .temp/converted-notebooks/*.py \
--max-line-length=$(NOTEBOOK_MAX_LINE_LENGTH) \
--disable=$(NOTEBOOK_PYLINT_EXCLUSIONS)
$(PYTHON) -m mypy .temp/converted-notebooks/*.py
dev-notebook-nbstripout:
$(VENV)/bin/nbstripout \
$(shell find ./notebooks -name *.ipynb)
dev-nbstripout-status:
$(VENV)/bin/nbstripout --status
dev-nbstripout-install:
$(VENV)/bin/nbstripout --install
dev-lint: dev-flake8 dev-pylint dev-mypy dev-notebook-lint
dev-unittest:
$(PYTHON) -m pytest -p no:cacheprovider $(ARGS) tests/unit_test
dev-peerscout-api-unittest:
$(PYTHON) -m pytest -p no:cacheprovider $(ARGS) tests_peerscout_api/unit_tests
dev-watch:
$(PYTHON) -m pytest_watch -- -p no:cacheprovider $(ARGS) $(PYTEST_WATCH_MODULES)
dev-test: dev-lint dev-unittest dev-peerscout-api-unittest
dev-run-peerscout-build-senior-editor-profiles:
$(PYTHON) -m data_science_pipeline.cli.peerscout_build_senior_editor_profiles
dev-run-sample-notebook:
$(PYTHON) -m papermill.cli \
./notebooks/example.ipynb \
/tmp/example-output.ipynb \
-p output_dataset $(OUTPUT_DATASET)
dev-peerscout-api-start:
$(PYTHON) -m \
peerscout_api.main \
--reload \
--factory \
--host 127.0.0.1 \
--port 8000
jupyter-build:
chmod a+w .
@if [ "$(NO_BUILD)" != "y" ]; then \
$(JUPYTER_DOCKER_COMPOSE) build jupyter; \
fi
jupyter-shell:
$(JUPYTER_RUN) bash $(ARGS)
jupyter-exec:
$(JUPYTER_DOCKER_COMPOSE) exec jupyter bash $(ARGS)
jupyter-container-update-dependencies:
$(JUPYTER_DOCKER_COMPOSE) exec jupyter \
pip install -r "$(PROJECT_FOLDER)/requirements.pipelines.txt"
jupyter-print-url:
@echo "jupyter url: http://localhost:$(DATA_SCIENCE_DAGS_JUPYTER_PORT)"
jupyter-start:
$(JUPYTER_DOCKER_COMPOSE) up -d jupyter
@$(MAKE) jupyter-print-url
jupyter-logs:
$(JUPYTER_DOCKER_COMPOSE) logs -f jupyter
jupyter-stop:
$(JUPYTER_DOCKER_COMPOSE) down
pylint:
$(DEV_RUN) python -m pylint data_science_pipeline tests setup.py
mypy:
$(DEV_RUN) python -m mypy data_science_pipeline tests setup.py
flake8:
$(DEV_RUN) python -m flake8 data_science_pipeline tests setup.py
notebook-lint:
$(JUPYTER_RUN) bash -c '\
cd .. \
&& pwd \
&& ls -l \
&& ls -l ./notebooks \
&& jupyter nbconvert \
--to=script \
--output-dir=./.temp/converted-notebooks/ \
./notebooks/**/*.ipynb \
&& pylint ./.temp/converted-notebooks/*.py \
--max-line-length=$(NOTEBOOK_MAX_LINE_LENGTH) \
--disable=$(NOTEBOOK_PYLINT_EXCLUSIONS) \
&& mypy ./.temp/converted-notebooks/*.py \
'
notebook-nbstripout-check:
$(JUPYTER_RUN) bash -c '\
cd .. \
&& pwd \
&& ls -l --recursive ./notebooks \
&& rm -rf /tmp/notebooks-nbstripout \
&& cp -r ./notebooks /tmp/notebooks-nbstripout \
&& nbstripout $$(find ./notebooks -name *.ipynb) \
&& ls -l --recursive /tmp/notebooks-nbstripout \
&& diff --recursive --brief /tmp/notebooks-nbstripout ./notebooks \
&& echo no unstripped notebook outputs found \
'
unittest:
$(DEV_RUN) python -m pytest -p no:cacheprovider $(ARGS) tests/unit_test
unittest-not-slow:
@$(MAKE) ARGS="$(ARGS) $(NOT_SLOW_PYTEST_ARGS)" unittest
.watch:
$(DEV_RUN) pytest-watch -- -p no:cacheprovider $(ARGS) $(PYTEST_WATCH_MODULES)
watch-slow:
@$(MAKE) .watch
watch:
@$(MAKE) ARGS="$(ARGS) $(NOT_SLOW_PYTEST_ARGS)" .watch
lint: flake8 pylint mypy notebook-lint
test: lint unittest
build:
$(DOCKER_COMPOSE) build data-science-pipelines
build-dev:
$(DOCKER_COMPOSE) build data-science-pipelines-dev
shell-dev:
$(DOCKER_COMPOSE) run --rm data-science-pipelines-dev bash
data-science-pipelines-run-peerscout-build-reviewing-editor-profiles:
$(DOCKER_COMPOSE) run --rm data-science-pipelines \
python -m data_science_pipeline.cli.peerscout_build_reviewing_editor_profiles
data-science-pipelines-run-peerscout-build-senior-editor-profiles:
$(DOCKER_COMPOSE) run --rm data-science-pipelines \
python -m data_science_pipeline.cli.peerscout_build_senior_editor_profiles
data-science-pipelines-run-peerscout-get-editor-pubmed-papers:
$(DOCKER_COMPOSE) run --rm data-science-pipelines \
python -m data_science_pipeline.cli.peerscout_get_editor_pubmed_papers \
--max-editors=$(MAX_EDITORS) \
--max-manuscripts=$(MAX_MANUSCRIPTS)
data-science-pipelines-run-peerscout-recommend-reviewing-editors:
$(DOCKER_COMPOSE) run --rm data-science-pipelines \
python -m data_science_pipeline.cli.peerscout_recommend_reviewing_editors \
--max-manuscripts=$(MAX_MANUSCRIPTS)
data-science-pipelines-run-peerscout-recommend-senior-editors:
$(DOCKER_COMPOSE) run --rm data-science-pipelines \
python -m data_science_pipeline.cli.peerscout_recommend_senior_editors \
--max-manuscripts=$(MAX_MANUSCRIPTS)
wait-for-peerscout-api:
docker-compose run --rm wait-for-it \
"peerscout-api:8080" \
--timeout=30 \
--strict\
-- echo "PeerScout API is up"
peerscout-api-build:
$(PEERSCOUT_API_DOCKER_COMPOSE) build peerscout-api
peerscout-api-start:
$(PEERSCOUT_API_DOCKER_COMPOSE) up -d peerscout-api
peerscout-api-start-and-wait:
$(MAKE) peerscout-api-start
$(MAKE) wait-for-peerscout-api
peerscout-api-end2end-test:
$(PEERSCOUT_API_DEV_DOCKER_PYTHON) -m pytest ./tests_peerscout_api/end2end_tests -v
peerscout-api-start-and-end2end-test: \
peerscout-api-start-and-wait peerscout-api-end2end-test
peerscout-api-stop:
$(PEERSCOUT_API_DOCKER_COMPOSE) down
peerscout-api-dev-start:
$(PEERSCOUT_API_DOCKER_COMPOSE) run --rm -p '8080:8080' -e FLASK_ENV=development peerscout-api
peerscout-api-dev-build:
$(PEERSCOUT_API_DOCKER_COMPOSE) build peerscout-api-dev
peerscout-api-dev-flake8:
$(PEERSCOUT_API_DEV_DOCKER_PYTHON) -m flake8 tests_peerscout_api peerscout_api
peerscout-api-dev-pylint:
$(PEERSCOUT_API_DEV_DOCKER_PYTHON) -m pylint tests_peerscout_api peerscout_api
peerscout-api-dev-mypy:
$(PEERSCOUT_API_DEV_DOCKER_PYTHON) -m mypy tests_peerscout_api peerscout_api
peerscout-api-dev-lint: \
peerscout-api-dev-flake8 peerscout-api-dev-pylint peerscout-api-dev-mypy
peerscout-api-dev-pytest:
$(PEERSCOUT_API_DEV_DOCKER_PYTHON) -m pytest ./tests_peerscout_api/unit_tests -v
peerscout-api-dev-pytest-watch:
$(PEERSCOUT_API_DEV_DOCKER_PYTHON) -m pytest_watch -- ./tests_peerscout_api/unit_tests -vv
peerscout-api-dev-test: \
peerscout-api-dev-lint peerscout-api-dev-pytest
clean:
$(DOCKER_COMPOSE) down -v
end2end-test:
$(MAKE) clean
$(DOCKER_COMPOSE) run --rm test-client
$(MAKE) clean
ci-build-main-image:
$(MAKE) DOCKER_COMPOSE="$(DOCKER_COMPOSE_CI)" \
build
ci-test-exclude-e2e:
$(DOCKER_COMPOSE) run --rm data-science-pipelines-dev ./run_test.sh
ci-build-and-test:
$(MAKE) DOCKER_COMPOSE="$(DOCKER_COMPOSE_CI)" \
build \
build-dev \
jupyter-build \
peerscout-api-build \
notebook-lint \
end2end-test \
peerscout-api-dev-build \
peerscout-api-dev-test \
peerscout-api-start-and-end2end-test
ci-clean:
$(DOCKER_COMPOSE_CI) down -v
retag-push-image:
docker tag $(EXISTING_IMAGE_REPO):$(EXISTING_IMAGE_TAG) $(IMAGE_REPO):$(IMAGE_TAG)
docker push $(IMAGE_REPO):$(IMAGE_TAG)