Merge pull request #1056 from cmu-delphi/release/delphi-epidata-0.4.4

Release Delphi Epidata 0.4.4

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.3
+current_version = 0.4.4
 commit = False
 tag = False
 
@@ -14,3 +14,5 @@ tag = False
 [bumpversion:file:src/client/packaging/pypi/setup.py]
 
 [bumpversion:file:src/client/packaging/pypi/delphi_epidata/__init__.py]
+
+[bumpversion:file:dev/local/setup.cfg]

.github/workflows/ci.yaml

@@ -51,8 +51,6 @@ jobs:
 
       - name: Build docker images
         run: |
-          docker build -t delphi_database -f repos/delphi/operations/dev/docker/database/Dockerfile .
-          docker build -t delphi_python -f repos/delphi/operations/dev/docker/python/Dockerfile .
           docker build -t delphi_database_epidata -f ./repos/delphi/delphi-epidata/dev/docker/database/epidata/Dockerfile .
           docker build -t delphi_web_python -f repos/delphi/delphi-epidata/dev/docker/python/Dockerfile .
           cd ./repos/delphi/delphi-epidata

dev/docker/database/epidata/Dockerfile

@@ -13,7 +13,7 @@ ENV MYSQL_ROOT_PASSWORD pass
 # create the `epidata` database
 ENV MYSQL_DATABASE epidata
 
-# create the `epi` user account with a development-only password
+# create the `user` account with a development-only password
 ENV MYSQL_USER user
 ENV MYSQL_PASSWORD pass
 

dev/docker/database/epidata/README.md

@@ -1,10 +1,10 @@
 # `delphi_database_epidata`
 
-This image extends Delphi's database by:
+This image extends a Percona database by:
 
-- adding the `epi` user account
-- adding the `epidata` database
-- creating empty tables in `epidata`
+- adding the `user` account
+- adding the `epidata` &  other appropriate databases
+- creating empty tables in those databases
 
 To start a container from this image, run:
 

dev/docker/python/Dockerfile

@@ -1,4 +1,11 @@
-# start with the `delphi_python` image
-FROM delphi_python
+FROM python:3.8-buster
 
-RUN pip install --no-cache-dir -r repos/delphi/delphi-epidata/requirements.txt -r repos/delphi/delphi-epidata/requirements.dev.txt
+WORKDIR /usr/src/app
+
+COPY repos repos
+COPY repos/delphi/delphi-epidata/dev/docker/python/setup.sh .
+
+RUN ln -s -f /usr/share/zoneinfo/America/New_York /etc/localtime && \
+    chmod -R o+r repos/ && \
+    bash setup.sh && \
+    pip install --no-cache-dir -r repos/delphi/delphi-epidata/requirements.api.txt -r repos/delphi/delphi-epidata/requirements.dev.txt

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

dev/local/Makefile

@@ -7,10 +7,6 @@
 #
 # Checks for the delphi-net bridge and creates if it doesn't exist.
 #
-# Creates all prereq images (delphi_database, delphi_python) only if they don't
-# exist. If you need to rebuild a prereq, you're probably doing something
-# complicated, and can figure out the rebuild command on your own.
-#
 #
 # Commands:
 #
@@ -78,7 +74,7 @@ web:
 	@# Build the web_epidata image
 	@cd repos/delphi/delphi-epidata;\
 		docker build -t delphi_web_epidata -f ./devops/Dockerfile .;\
-		cd ../../../
+		cd -
 
 	@# Run the web server
 	@docker run --rm -p 127.0.0.1:10080:80 \
@@ -97,10 +93,6 @@ db:
 	@# Setup virtual network if it doesn't exist
 	@docker network ls | grep delphi-net || docker network create --driver bridge delphi-net
 
-	@# Only build prereqs if we need them
-	@docker images delphi_database | grep delphi || \
-		docker build -t delphi_database -f repos/delphi/operations/dev/docker/database/Dockerfile .
-
 	@# Build the database_epidata image
 	@docker build -t delphi_database_epidata \
 		-f repos/delphi/delphi-epidata/dev/docker/database/epidata/Dockerfile .
@@ -120,10 +112,6 @@ db:
 
 .PHONY=py
 py:
-	@# Build the python image
-	@docker build -t delphi_python \
-		-f repos/delphi/operations/dev/docker/python/Dockerfile .
-
 	@docker build -t delphi_web_python \
 		-f repos/delphi/delphi-epidata/dev/docker/python/Dockerfile .
 

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 0.4.0
+version = 0.4.4
 
 [options]
 packages =

devops/Dockerfile

@@ -5,25 +5,25 @@ RUN npm ci && npm run build
 
 FROM tiangolo/meinheld-gunicorn:python3.8
 LABEL org.opencontainers.image.source=https://github.com/cmu-delphi/delphi-epidata
-# use delphi's timezome
-RUN ln -s -f /usr/share/zoneinfo/America/New_York /etc/localtime
 
-COPY requirements.txt /app/requirements_also.txt
-RUN pip install --no-cache-dir -r /tmp/requirements.txt -r requirements_also.txt
+COPY ./devops/gunicorn_conf.py /app
+COPY ./devops/start_wrapper.sh /
+COPY ./src/server/ /app/app/
+COPY --from=builder ./src/build/lib/ /app/app/lib/
+
+COPY requirements.api.txt /app/requirements_also.txt
+
+RUN ln -s -f /usr/share/zoneinfo/America/New_York /etc/localtime \
+      && rm -rf /app/app/__pycache__ /app/app/*.php \
+      && chmod -R o+r /app/app \
+      && chmod 755 /start_wrapper.sh \
+      && pip install --no-cache-dir -r /tmp/requirements.txt -r requirements_also.txt
 # the file /tmp/requirements.txt is created in the parent docker definition.  (see:
 #   https://github.com/tiangolo/meinheld-gunicorn-docker/blob/master/docker-images/python3.8.dockerfile#L5 )
 # this combined requirements installation ensures all version constrants are accounted for.
 
 # disable python stdout buffering
 ENV PYTHONUNBUFFERED 1
 
-COPY ./devops/gunicorn_conf.py /app
-COPY ./devops/start_wrapper.sh /
-COPY ./src/server/ /app/app/
-COPY --from=builder ./src/build/lib/ /app/app/lib/
-RUN rm -rf /app/app/__pycache__ /app/app/*.php \
-      && chmod -R o+r /app/app \
-      && chmod 755 /start_wrapper.sh
-
 ENTRYPOINT [ "/entrypoint.sh" ]
 CMD [ "/start_wrapper.sh" ]

docs/Gemfile.lock

@@ -211,7 +211,7 @@ GEM
       jekyll-seo-tag (~> 2.1)
     minitest (5.14.4)
     multipart-post (2.1.1)
-    nokogiri (1.13.9)
+    nokogiri (1.13.10)
       mini_portile2 (~> 2.8.0)
       racc (~> 1.4)
     octokit (4.20.0)
@@ -220,7 +220,7 @@ GEM
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
     public_suffix (4.0.6)
-    racc (1.6.0)
+    racc (1.6.1)
     rb-fsevent (0.10.4)
     rb-inotify (0.10.1)
       ffi (~> 1.0)