System: update delphi_web_python Docker image

- merge operations repo delphi_python Dockerfile into delphi_web_python
- copy Python requirements file to this directory
- copy setup.sh to this directory

Author: dshemetov

dev/docker/python/Dockerfile

@@ -1,4 +1,22 @@
 # start with the `delphi_python` image
-FROM delphi_python
+FROM python:3.8-buster
+
+# use delphi's timezome
+RUN ln -s -f /usr/share/zoneinfo/America/New_York /etc/localtime
+
+# specify a working directory inside the container
+WORKDIR /usr/src/app
+
+# install python packages
+COPY repos/delphi/delphi-epidata/dev/docker/python/requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+
+# copy over all source files
+COPY repos repos
+RUN chmod -R o+r repos/
+
+# configure the image to match the delphi server
+COPY repos/delphi/delphi-epidata/dev/docker/python/setup.sh .
+RUN bash setup.sh
 
 RUN pip install --no-cache-dir -r repos/delphi/delphi-epidata/requirements.txt -r repos/delphi/delphi-epidata/requirements.dev.txt

dev/docker/python/requirements.txt

@@ -0,0 +1,31 @@
+aiohttp
+beautifulsoup4
+covidcast
+delphi_utils
+docker
+dropbox
+epiweeks
+Flask==1.1.2
+freezegun
+google-api-python-client
+lxml
+matplotlib
+mysql-connector
+mysqlclient==2.0.2
+newrelic
+numpy
+orjson==3.4.7
+pandas==1.2.3
+pycountry
+pymysql
+pytest
+pytest-check
+python-dotenv==0.15.0
+requests
+sas7bdat
+scikit-learn
+scipy==1.6.2
+selenium
+SQLAlchemy==1.3.22
+structlog
+xlrd

dev/docker/python/setup.sh

@@ -0,0 +1,27 @@
+# This script sets up the correct directory structure within the `delphi_img`
+# docker image.
+
+# Some notes on package structure:
+#   - Python package names can't contain hyphens, so hyphens in repo names are
+#     replaced with underscores in the package hierarchy. (An exception is the
+#     repo `delphi-epidata`, which is renamed to simply `epidata`.)
+#   - Repos are organized such that the main code for the package is inside of
+#     a `src/` directory. When deployed, `src/` is elided. (An exception is the
+#     legacy `undef-analysis` repo, which has sources at the top-level.)
+
+# bail if anything fails
+set -e
+
+# create python package `undefx`
+mkdir undefx
+mv repos/undefx/py3tester/src undefx/py3tester
+mv repos/undefx/undef-analysis undefx/undef_analysis
+
+# create python package `delphi`
+mkdir delphi
+mv repos/delphi/operations/src delphi/operations
+mv repos/delphi/utils/src delphi/utils
+mv repos/delphi/github-deploy-repo/src delphi/github_deploy_repo
+mv repos/delphi/delphi-epidata/src delphi/epidata
+mv repos/delphi/flu-contest/src delphi/flu_contest
+mv repos/delphi/nowcast/src delphi/nowcast