Initial commit

.flake8

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+[flake8]
+ignore = E203, E501, W503
+max-line-length = 99

.github/workflows/build-containers.yml

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+
+name: Build and publish container
+
+on:
+  push:
+    branches: [main]
+    paths: ['runtime/**', '.github/workflows/build-containers.yml']
+  pull_request:
+    paths: ['runtime/**', '.github/workflows/build-containers.yml']
+
+jobs:
+  build:
+    name: Build, Test, Publish container
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest']
+        proc: ['cpu', 'gpu']
+    env:
+      CONTAINER: drivendata/floodwater-competition
+      SHA_TAG: ${{ matrix.proc }}-${{ github.sha }}
+      LATEST_TAG: ${{ matrix.proc }}-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Build ${{ matrix.proc }} container
+        run: |
+          docker build runtime --build-arg CPU_OR_GPU=${{ matrix.proc }} --tag $CONTAINER:$SHA_TAG
+          docker build runtime --build-arg CPU_OR_GPU=${{ matrix.proc }} --tag $CONTAINER:$LATEST_TAG
+
+      - name: Tests container packages
+        run: |
+          docker run $CONTAINER:$SHA_TAG /bin/bash -c "conda run --no-capture-output -n condaenv pytest tests/test_packages.py"
+
+      - name: Login to DockerHub
+        if: github.ref == 'refs/heads/main'
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Publish container if main branch
+        if: github.ref == 'refs/heads/main'
+        run: |
+          docker push $CONTAINER:$SHA_TAG
+          docker push $CONTAINER:$LATEST_TAG

.github/workflows/test-makefile.yml

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+
+name: Test Makefile
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  build:
+    name: Pull images, pack benchmark, test-submission
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest']
+        proc: ['cpu']
+    env:
+      CONTAINER: drivendataorg/deid2-competition
+      SHA_TAG: ${{ matrix.proc }}-${{ github.sha }}
+      LATEST_TAG: ${{ matrix.proc }}-latest
+      GITHUB_ACTIONS_NO_TTY: true
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Test zipping benchmark
+        run: |
+          make pack-benchmark
+
+      - name: Pull latest image and run submission in container
+        run: |
+          make pull
+          make test-submission

.gitignore

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+# Basics
+*.py[cod]
+*.pyc
+__pycache__
+
+# OSX
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Logs
+logs
+*.log
+pip-log.txt
+npm-debug.log*
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+htmlcov/
+coverage.xml
+
+# Vim
+*~
+*.swp
+*.swo
+
+# SublimeText
+# cache files for sublime text
+*.tmlanguage.cache
+*.tmPreferences.cache
+*.stTheme.cache
+
+# workspace files are user-specific
+*.sublime-workspace
+
+# Docker
+.cache/
+
+# .docker folders
+*.docker/
+
+# Ignore notebook temp files
+**/.ipynb_checkpoints/
+
+# local env files
+.env*
+.env.local
+.env.*.local
+
+# Editor directories and files
+.idea
+.vscode
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw*
+
+# package stuff
+src.egg-info/
+pip-wheel-metadata/
+*.egg-info/
+
+# Submissions
+submission/

Makefile

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+.PHONY: build debug-container export-requirements pack-benchmark pull resolve-requirements test-container test-submission unpin-requirements
+
+# ================================================================================================
+# Settings
+# ================================================================================================
+
+ifeq (, $(shell which nvidia-smi))
+CPU_OR_GPU ?= cpu
+else
+CPU_OR_GPU ?= gpu
+endif
+
+ifeq (${CPU_OR_GPU}, gpu)
+GPU_ARGS = --gpus all
+endif
+
+SKIP_GPU ?= false
+ifeq (${SKIP_GPU}, true)
+GPU_ARGS =
+endif
+
+REPO = drivendata/floodwater-competition
+
+TAG = ${CPU_OR_GPU}-latest
+LOCAL_TAG = ${CPU_OR_GPU}-local
+
+IMAGE = ${REPO}:${TAG}
+LOCAL_IMAGE = ${REPO}:${LOCAL_TAG}
+
+# if not TTY (for example GithubActions CI) no interactive tty commands for docker
+ifneq (true, ${GITHUB_ACTIONS_NO_TTY})
+TTY_ARGS = -it
+endif
+
+# To run a submission, use local version if that exists; otherwise, use official version
+# setting SUBMISSION_IMAGE as an environment variable will override the image
+SUBMISSION_IMAGE ?= $(shell docker images -q ${LOCAL_IMAGE})
+ifeq (,${SUBMISSION_IMAGE})
+SUBMISSION_IMAGE := $(shell docker images -q ${IMAGE})
+endif
+
+# Give write access to the submission folder to everyone so Docker user can write when mounted
+_submission_write_perms:
+	chmod -R 0777 submission/
+
+# ================================================================================================
+# Commands for building the container if you are changing the requirements
+# ================================================================================================
+
+## Builds the container locally, tagging it with cpu-local or gpu-local
+build:
+	docker build --build-arg CPU_OR_GPU=${CPU_OR_GPU} -t ${LOCAL_IMAGE} runtime
+
+# ================================================================================================
+# Commands for testing that your submission.zip will execute
+# ================================================================================================
+
+## Pulls the official container tagged cpu-latest or gpu-latest from Docker hub
+pull:
+	docker pull ${IMAGE}
+
+## Creates a submission/submission.zip file from whatever is in the "benchmark" folder
+pack-benchmark:
+# Don't overwrite so no work is lost accidentally
+ifneq (,$(wildcard ./submission/submission.zip))
+	$(error You already have a submission/submission.zip file. Rename or remove that file (e.g., rm submission/submission.zip).)
+endif
+	cd benchmark; zip -r ../submission/submission.zip ./*
+
+
+## Runs container with submission/submission.zip as your submission and data as the data to work with
+test-submission: _submission_write_perms
+
+# if submission file does not exist
+ifeq (,$(wildcard ./submission/submission.zip))
+	$(error To test your submission, you must first put a "submission.zip" file in the "submission" folder. \
+	  If you want to use the benchmark, you can run `make pack-benchmark` first)
+endif
+
+# if container does not exists, error and tell user to pull or build
+ifeq (${SUBMISSION_IMAGE},)
+	$(error To test your submission, you must first run `make pull` (to get official container) or `make build` \
+		(to build a local version if you have changes).)
+endif
+	docker run \
+		${TTY_ARGS} \
+		${GPU_ARGS} \
+		--network none \
+		--mount type=bind,source="$(shell pwd)"/runtime/data,target=/codeexecution/data,readonly \
+		--mount type=bind,source="$(shell pwd)"/runtime/tests,target=/codeexecution/tests,readonly \
+		--mount type=bind,source="$(shell pwd)"/runtime/entrypoint.sh,target=/codeexecution/entrypoint.sh \
+		--mount type=bind,source="$(shell pwd)"/submission,target=/codeexecution/submission \
+		--shm-size 8g \
+		${SUBMISSION_IMAGE}
+
+
+#################################################################################
+# Self Documenting Commands                                                     #
+#################################################################################
+
+.DEFAULT_GOAL := help
+.PHONY: help
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+pattern = re.compile(r'^## (.*)\n(.+):', re.MULTILINE)
+text = "".join(line for line in sys.stdin)
+for match in pattern.finditer(text):
+    help, target = match.groups()
+    print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)