Simulation scenarios, TLO CLI, interaction with Azure Batch (#249)

Co-authored-by: Mosè Giordano <[email protected]>
Co-authored-by: Tim Hallett <[email protected]>

.gitignore

@@ -109,3 +109,7 @@ venv.bak/
 # TLO .rst files
 docs/reference/tlo*.rst
 
+# TLO configuration
+tlo.conf
+
+

MANIFEST.in

@@ -7,9 +7,11 @@ include README.rst
 include .bumpversion.cfg
 include .coveragerc
 include tox.ini .travis.yml
+include tlo.example.conf
 
 exclude .editorconfig
 recursive-exclude .ci *
+recursive-exclude deploy *
 recursive-exclude outputs *
 recursive-exclude resources *
 

deploy/.gitignore

@@ -0,0 +1 @@
+/id_ed25519

deploy/Dockerfile

@@ -0,0 +1,26 @@
+FROM python:3.8-slim-buster
+
+# Setup SSH
+RUN mkdir /root/.ssh
+COPY id_ed25519 /root/.ssh/id_ed25519
+COPY known_hosts /root/.ssh/known_hosts
+RUN chmod -R 0600 /root/.ssh
+
+# Install Git, Git LFS.  How to silence apt-get commands:
+# https://peteris.rocks/blog/quiet-and-unattended-installation-with-apt-get/
+RUN apt-get update -qq
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -qq -y git git-lfs < /dev/null > /dev/null
+# Cleanup apt cache
+RUN rm -rf /var/lib/apt/lists/*
+# Configure git lfs
+RUN git lfs install
+
+# Clone the TLOModel repository and move in it
+ARG BRANCH_NAME="master"
+RUN git clone --branch "${BRANCH_NAME}" [email protected]:UCL/TLOmodel.git /TLOmodel
+WORKDIR /TLOmodel
+RUN git gc --aggressive
+
+# Install dependencies
+RUN pip3 install -r requirements/dev.txt
+RUN pip3 install -e .

deploy/deploy.sh

@@ -0,0 +1,27 @@
+#!/bin/sh
+
+set -e
+
+REGISTRY_NAME="tlomodel"
+REGISTRY_URL="${REGISTRY_NAME}.azurecr.io"
+IMAGE_NAME="tlo"
+IMAGE_TAG="1.0"
+IMAGE_FULL_NAME="${IMAGE_NAME}:${IMAGE_TAG}"
+
+# Documentation at
+# https://docs.microsoft.com/en-us/azure/container-registry/container-registry-get-started-docker-cli.
+
+# Login to Azure Container Registry
+echo -n "Logging into ${REGISTRY_NAME}..."
+az acr login --name "${REGISTRY_NAME}"
+echo "done"
+# Build the image
+echo "Building docker image ${IMAGE_FULL_NAME}..."
+docker build --tag "${IMAGE_FULL_NAME}" .
+# Tag the image
+echo -n "Tagging ${REGISTRY_URL}/${IMAGE_FULL_NAME}..."
+docker tag "${IMAGE_FULL_NAME}" "${REGISTRY_URL}/${IMAGE_FULL_NAME}"
+echo "done"
+# Push the image
+echo "Pushing ${REGISTRY_URL}/${IMAGE_FULL_NAME}..."
+docker push "${REGISTRY_URL}/${IMAGE_FULL_NAME}"

deploy/id_ed25519.pub

@@ -0,0 +1 @@
+ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIC+bU4n6EHIFRqTI1617bR9A54WLjawxGow+X7Rvb1M6 [email protected]

deploy/known_hosts

@@ -0,0 +1 @@
+|1|/L/ftN7pdpk7XqhXWGqqXFDK9yQ=|0IcBIB1SvDcSoXcKhpsmvWRkHDw= ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAq2A7hRGmdnm9tUDbO9IDSwBK6TbQa+PXYPCPy6rbTrTtw7PHkccKrpp0yVhp5HdEIcKr6pLlVDBfOLX9QUsyCOV0wzfjIJNlGEYsdlLJizHhbn2mUjvSAHQqZETYP81eFzLQNnPHt4EVVUh7VfDESU84KezmD5QlWpXLmvU31/yMf+Se8xhHTvKSCZIFImWwoG6mbUoWf9nzpIoaSjB+weqqUUmpaaasXVal72J+UX2B+2RPW3RcT0eOzQgqlJL3RKrTJvdsjE3JEAvGq3lGHSZXy28G3skua2SmVi/w4yCE6gbODqnTWlg7+wC604ydGXA8VJiS5ap43JXiUFFAaQ==

requirements/base.in

@@ -1,6 +1,14 @@
 # Base requirements file - common packages we use directly
 
+GitPython
+click
 numpy
 pandas
 scipy
 openpyxl
+
+# To submit jobs to Azure Batch
+azure-batch
+azure-identity
+azure-keyvault
+azure-storage-file-share

requirements/base.txt

@@ -4,24 +4,125 @@
 #
 #    pip-compile --output-file=base.txt base.in
 #
+adal==1.2.6
+    # via msrestazure
+azure-batch==10.0.0
+    # via -r base.in
+azure-common==1.1.26
+    # via
+    #   azure-batch
+    #   azure-keyvault-certificates
+    #   azure-keyvault-keys
+    #   azure-keyvault-secrets
+azure-core==1.11.0
+    # via
+    #   azure-identity
+    #   azure-keyvault-certificates
+    #   azure-keyvault-keys
+    #   azure-keyvault-secrets
+    #   azure-storage-file-share
+azure-identity==1.5.0
+    # via -r base.in
+azure-keyvault-certificates==4.2.1
+    # via azure-keyvault
+azure-keyvault-keys==4.3.1
+    # via azure-keyvault
+azure-keyvault-secrets==4.2.0
+    # via azure-keyvault
+azure-keyvault==4.1.0
+    # via -r base.in
+azure-storage-file-share==12.4.1
+    # via -r base.in
+certifi==2020.12.5
+    # via
+    #   msrest
+    #   requests
+cffi==1.14.5
+    # via cryptography
+chardet==4.0.0
+    # via requests
+click==7.1.2
+    # via -r base.in
+cryptography==3.4.6
+    # via
+    #   adal
+    #   azure-identity
+    #   azure-keyvault-keys
+    #   azure-storage-file-share
+    #   msal
+    #   pyjwt
 et-xmlfile==1.0.1
     # via openpyxl
+gitdb==4.0.5
+    # via gitpython
+gitpython==3.1.13
+    # via -r base.in
+idna==2.10
+    # via requests
+isodate==0.6.0
+    # via msrest
 jdcal==1.4.1
     # via openpyxl
-numpy==1.19.5
+msal-extensions==0.3.0
+    # via azure-identity
+msal==1.9.0
+    # via
+    #   azure-identity
+    #   msal-extensions
+msrest==0.6.21
+    # via
+    #   azure-batch
+    #   azure-keyvault-certificates
+    #   azure-keyvault-keys
+    #   azure-keyvault-secrets
+    #   azure-storage-file-share
+    #   msrestazure
+msrestazure==0.6.4
+    # via azure-batch
+numpy==1.20.1
     # via
     #   -r base.in
     #   pandas
     #   scipy
+oauthlib==3.1.0
+    # via requests-oauthlib
 openpyxl==3.0.6
     # via -r base.in
-pandas==1.2.1
+pandas==1.2.2
     # via -r base.in
+portalocker==1.7.1
+    # via msal-extensions
+pycparser==2.20
+    # via cffi
+pyjwt[crypto]==2.0.1
+    # via
+    #   adal
+    #   msal
 python-dateutil==2.8.1
+    # via
+    #   adal
+    #   pandas
+pytz==2021.1
     # via pandas
-pytz==2020.5
-    # via pandas
-scipy==1.6.0
+requests-oauthlib==1.3.0
+    # via msrest
+requests==2.25.1
+    # via
+    #   adal
+    #   azure-core
+    #   msal
+    #   msrest
+    #   requests-oauthlib
+scipy==1.6.1
     # via -r base.in
 six==1.15.0
-    # via python-dateutil
+    # via
+    #   azure-core
+    #   azure-identity
+    #   isodate
+    #   msrestazure
+    #   python-dateutil
+smmap==3.0.5
+    # via gitdb
+urllib3==1.26.3
+    # via requests