Integrate with nnfabrik

.dockerignore

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+data

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+data/
+.ssh/
+.idea/

Dockerfile

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+FROM sinzlab/pytorch:v3.8-torch1.4.0-cuda10.1-dj0.12.4 as intermediate
+
+WORKDIR /
+COPY .ssh/id_rsa .
+# Need to change the permissions of the private key because otherwise they are too open if the key is copied from
+# Windows
+RUN chmod 400 id_rsa && \
+    eval $(ssh-agent) && \
+    ssh-add id_rsa && \
+    ssh-keyscan -H github.com >> /etc/ssh/ssh_known_hosts && \
+    git clone git@github.com:sinzlab/nnfabrik /src/nnfabrik && \
+    git clone git@github.com:sinzlab/ml-utils /src/ml-utils
+
+
+
+FROM sinzlab/pytorch:v3.8-torch1.4.0-cuda10.1-dj0.12.4
+
+COPY --from=intermediate /src /src
+WORKDIR /src
+RUN python3 -m pip install ./nnfabrik && \
+    python3 -m pip install ./ml-utils
+
+RUN apt-get update && apt-get install -y nodejs npm
+RUN jupyter labextension install jupyterlab_vim
+
+WORKDIR /src/mei
+COPY . .
+RUN python3 -m pip install -e .

docker-compose.yml

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+version: "3.7"
+services:
+  pycharm:
+      build: .
+      volumes:
+      - .:/src/mei
+      - ./data:/data
+      entrypoint: ""
+  jupyter:
+      build: .
+      volumes:
+      - .:/src/mei
+      - ./data:/data
+      ports:
+      - 8888:8888
+      env_file:
+        - .env

docker-compose.yml.jinja

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+{% set common %}
+    build: .
+    volumes:
+        - .:/src/mei
+        - ./data:/data
+    env_file:
+        - .env
+    ipc: host
+{% endset %}
+
+version: '2.3'
+services:
+    {% for i in range(N_GPU) %}
+    gpu{{ i }}:
+        {{ common|indent(4, True) }}
+        ports:
+            - 1004{{ i }}:8888
+        container_name: "dev_cblessing_mei_gpu{{ i }}"
+        environment:
+            - NVIDIA_VISIBLE_DEVICES={{ i }}
+        runtime: nvidia
+    {% endfor %}
+    cpu:
+        {{ common|indent(4, True) }}
+        ports:
+            - 10051:8888
+        container_name: "dev_cblessing_mei_cpu"
+        runtime: runc