#510 second PoC - GHC with pixi for Docker using pyproject.toml

Author: justb4

.dockerignore

@@ -1 +1,18 @@
+# VCS
 .git
+.gitignore
+
+# Local pixi environment (built inside the image via `pixi install`)
+.pixi
+
+# Local dev / bootstrap artifacts (regenerated in the image)
+instance
+report.md
+docs/_build
+GeoHealthCheck/static/lib
+GeoHealthCheck/data.db
+
+# Tooling / caches
+.pytest_cache
+**/__pycache__
+*.pyc

.flake8

@@ -1,4 +1,4 @@
 [flake8]
 max-line-length = 79
-exclude = .git,.cache,docs,docker,build,dist,GeoHealthCheck/migrations
+exclude = .git,.cache,docs,docker,build,dist,.pixi,GeoHealthCheck/migrations
 # max-complexity = 38

.gitignore

@@ -63,6 +63,9 @@ GeoHealthCheck.conf
 
 # Data
 GeoHealthCheck/data.db
+# test report
+report.md
+
 # pixi environments
 .pixi/*
 !.pixi/config.toml

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:noble
+FROM ghcr.io/prefix-dev/pixi:0.72.0-noble
 
 # Credits to yjacolin for providing first versions
 LABEL original_developer="yjacolin <yves.jacolin@camptocamp.com>" \
@@ -18,14 +18,15 @@ ENV LC_ALL="en_US.UTF-8" \
 	LANGUAGE="en_US.UTF-8" \
     \
 	\
-	DEB_PACKAGES="locales gunicorn python3.12-venv postgresql-client python3-gunicorn python3-gevent python3-lxml python3-pyproj" \
-	DEB_BUILD_DEPS="make python3-pip" \
+	DEB_PACKAGES="ca-certificates locales postgresql-client" \
+	DEB_BUILD_DEPS="curl adduser" \
 	ADMIN_NAME=admin \
 	ADMIN_PWD=admin \
 	ADMIN_EMAIL=admin.istrator@mydomain.com \
 	SQLALCHEMY_DATABASE_URI='sqlite:////GeoHealthCheck/DB/data.db' \
 	SQLALCHEMY_ENGINE_OPTION_PRE_PING=False \
 	SECRET_KEY='d544ccc37dc3ad214c09b1b7faaa64c60351d5c8bb48b342' \
+	GHC_HOME=/GeoHealthCheck \
 	GHC_PROBE_HTTP_TIMEOUT_SECS=30 \
 	GHC_MINIMAL_RUN_FREQUENCY_MINS=10 \
 	GHC_RETENTION_DAYS=30 \
@@ -72,30 +73,34 @@ WSGI_WORKER_CLASS='gevent' \
 # GHC User Plugins, best be overridden via Container environment \
 GHC_USER_PLUGINS=''
 
-# Install operating system dependencies
-RUN \
-    apt-get update \
-    && apt-get --no-install-recommends install -y ${DEB_PACKAGES} ${DEB_BUILD_DEPS} ${ADD_DEB_PACKAGES} \
-    && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8 \
-    && echo "For ${TZ} date=$(date)" && echo "Locale=$(locale)"
-
 # Add standard files and Add/override Plugins
 # Alternative Entrypoints to run GHC jobs
 # Override default Entrypoint with these on Containers
 COPY docker/scripts/*.sh docker/config_site.py docker/plugins /
 
 # Add Source Code
-COPY . /GeoHealthCheck
+COPY . ${GHC_HOME}
 
-# Install
+WORKDIR ${GHC_HOME}
+
+# Install operating system dependencies
 RUN \
-	chmod a+x /*.sh && ./install.sh \
-    # Cleanup TODO: remove unused Locales and TZs \
+    apt-get update \
+    && apt-get --no-install-recommends install -y ${DEB_PACKAGES} ${DEB_BUILD_DEPS} ${ADD_DEB_PACKAGES} \
+    && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8 \
+    && echo "For ${TZ} date=$(date)" && echo "Locale=$(locale)"  \
+    && adduser --disabled-password --shell /bin/bash --home ${GHC_HOME} --gecos "User" ghc \
+    && chmod +x /*.sh  \
+    && echo "pixi install --locked -e prod" && pixi install --locked -e prod \
+    && echo "pixi run -e prod setup" && pixi run -e prod setup \
+    && echo "cp /config_site.py " && cp /config_site.py ${GHC_HOME}/instance/config_site.py \
+    && echo "copy plugins.." && if [ -d /plugins ]; then cp -ar /plugins/* ${GHC_HOME}/GeoHealthCheck/plugins/; fi && rm -rf /plugins \
     && apt-get remove --purge -y ${DEB_BUILD_DEPS} \
     && apt-get clean \
     && apt autoremove -y  \
     && rm -rf /var/lib/apt/lists/*
 
+# USER ghc
 
 # For SQLite
 VOLUME ["/GeoHealthCheck/DB/"]

README.md

@@ -69,30 +69,56 @@ python3 GeoHealthCheck/models.py load <.json data file> [y/n]
 
 ## Install with Pixi
 
+[Pixi](https://pixi.sh) manages the environment; tasks run via `pixi run`,
+so no shell activation is needed.
+
 ```
 git clone https://github.com/geopython/GeoHealthCheck.git
 cd GeoHealthCheck
 
 # Install production environment
 pixi install -e prod
-pixi shell -e prod
-invoke setup
+
+# bootstrap the app (config, static assets, i18n, local docs, DB)
+pixi run -e prod setup
 
 # generate secret key
-invoke create-secret-key
+pixi run -e prod create-secret-key
 # setup local configuration (overrides GeoHealthCheck/config_main.py)
 vi instance/config_site.py
 # edit at least secret key:
-# - SECRET_KEY  # copy/paste result string from `invoke create-secret-key`
+# - SECRET_KEY  # copy/paste result string from the command above
 
 # Optional: edit other settings or leave defaults (see above)
 
-# setup superuser account passsword and email directly 
-invoke create admin admin a@a.com
+# setup superuser account password and email directly
+pixi run -e prod create -username admin -password admin --email a@a.com
+
+# or shorter
+pixi run -e prod create -u admin -p admin --e a@a.com
 
 # run locally
-python GeoHealthCheck/app.py  
+pixi run -e prod run
+ 
+# open http://localhost:8000 in browser
+
+```
+
+### Development and tests
 
 ```
+# install the dev environment (adds flake8, pytest, ...)
+pixi install -e dev
+
+# bootstrap once, needed before the tests can run
+pixi run -e dev setup
+
+# run the unit tests
+pixi run -e dev test
+```
+
+Prefer an interactive shell? `pixi shell -e prod` (or `-e dev`) activates the
+environment, after which `invoke ...` and `python ...` work directly.
+
 
 More in the [full GHC documentation](http://docs.geohealthcheck.org/).

docker/compose/docker-compose.yml

@@ -4,7 +4,6 @@
 # configured in the GHC Web App.
 #
 # Plugins (optional) need to be configured for both Docker containers.
-version: "3"
 
 services:
   ghc_web:

docker/scripts/configure.sh

@@ -9,13 +9,12 @@ export PYTHONPATH=/GeoHealthCheck/GeoHealthCheck:$PYTHONPATH
 # Determine database type from DB URI
 DB_TYPE=$(echo ${SQLALCHEMY_DATABASE_URI} | cut -f1 -d:)
 echo "Using DB_TYPE=${DB_TYPE}"
+# pixi shell -e prod
 
 # Create DB shorthand
 function create_db() {
 	pushd /GeoHealthCheck/  || exit 1
-	source bin/activate
-
-	invoke create -u ${ADMIN_NAME} -p ${ADMIN_PWD} -e ${ADMIN_EMAIL}
+  pixi run -e prod create -u ${ADMIN_NAME} -p ${ADMIN_PWD} -e ${ADMIN_EMAIL}
 	popd || exit 1
 }
 

docker/scripts/install.sh

@@ -12,7 +12,6 @@ echo "START /run-runner.sh"
 export PYTHONPATH=/GeoHealthCheck/GeoHealthCheck:$PYTHONPATH
 
 cd /GeoHealthCheck
-source bin/activate
-invoke runner-daemon
+pixi run -e prod runner-daemon
 
 echo "END /run-runner.sh"