GalaxyBenchmarker V2 for storage benchmarking

.dockerignore

@@ -0,0 +1,7 @@
+# GalaxyBenchmarker generated files
+logs/
+results/
+
+# Python stuff
+venv/
+.venv/

.gitignore

@@ -7,6 +7,8 @@ tools.yml
 *.html
 results/*
 tool_test_output.*
+.vscode
+evaluation/*.png
 
 ### Autogenerated: ###
 # Byte-compiled / optimized / DLL files

Dockerfile

@@ -1,8 +1,28 @@
-FROM python:3.7
+FROM python:3.10
 
-COPY requirements.txt ./
-RUN pip install --no-cache-dir -r requirements.txt
-RUN pip uninstall bioblend -y
-RUN git clone https://github.com/galaxyproject/bioblend.git && cd bioblend && python setup.py install
+ENV PIP_NO_CACHE_DIR=1 \
+  PIP_DISABLE_PIP_VERSION_CHECK=1
 
-RUN cd / && git clone https://github.com/usegalaxy-eu/workflow-testing.git
+RUN \
+  apt-get update \
+  && apt-get install -y \
+    rsync \
+    tini \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/* /tmp/*
+
+RUN pip install poetry
+
+WORKDIR /src
+COPY poetry.lock pyproject.toml /src/
+
+RUN poetry config virtualenvs.create false \
+  && poetry install --no-dev --no-interaction --no-ansi
+
+RUN git clone https://github.com/usegalaxy-eu/workflow-testing.git /workflow-testing
+
+COPY . /src/
+
+COPY scripts/entrypoint.sh /entrypoint.sh
+
+ENTRYPOINT ["/usr/bin/tini", "-v", "--", "/entrypoint.sh"]

Makefile

@@ -0,0 +1,36 @@
+run:
+	docker-compose up -d
+	docker-compose logs -f benchmarker
+
+run_sudo:
+	sudo -E docker-compose up -d
+	sudo docker-compose logs -f benchmarker
+
+.PHONY: run_cron
+run_cron:
+	/usr/local/bin/docker-compose up -d
+
+stop:
+	echo "Gracefull shutdown. Benchmarker has 30 seconds to save results"
+	docker-compose stop -t 30 benchmarker
+
+stop_sudo:
+	echo "Gracefull shutdown. Benchmarker has 30 seconds to save results"
+	sudo docker-compose stop -t 30 benchmarker
+
+build:
+	docker-compose build
+
+build_sudo:
+	sudo docker-compose build
+
+lint: lint_isort lint_black
+
+lint_isort:
+	poetry run isort galaxy_benchmarker
+
+lint_black:
+	poetry run black --target-version py310 galaxy_benchmarker
+
+lint_mypy:
+	poetry run mypy galaxy_benchmarker