Improve the surface of pixi integration

.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,.pixi,docs,docker,build,dist,GeoHealthCheck/migrations
 # max-complexity = 38

.github/workflows/main.yml

@@ -2,6 +2,7 @@
 # https://github.com/geopython/pycsw/blob/master/.github/workflows/main.yml
 #
 # Author: Just van den Broecke - 2021
+# Migrated to pixi - 2026
 #
 name: Main GHC CI ⚙️
 
@@ -10,44 +11,44 @@ on: [ push, pull_request ]
 jobs:
   main:
     runs-on: ubuntu-24.04
-    strategy:
-      matrix:
-        include:
-          - python-version: 3.12.3
     steps:
     - name: Checkout ✅
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
-    - name: Setup Python ${{ matrix.python-version }} 🐍
-      uses: actions/setup-python@v2
+    # Installs pixi (pinned) and the `dev` environment from the committed
+    # pixi.lock (locked: true fails if the lock is out of sync). Python and
+    # all dependencies come from the lock, so no separate setup-python step.
+    - name: Setup pixi 🧰
+      uses: prefix-dev/setup-pixi@v0.10.0
       with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install Requirements 📦
-      run: |
-        python -m pip install --upgrade pip
-        pip3 install -r requirements.txt
-        pip3 install -r requirements-dev.txt
+        pixi-version: v0.72.0
+        environments: dev
+        locked: true
+        cache: true
 
     - name: Setup GHC App and init DB 🗃️
       run: |
-        invoke setup
-        echo -e "admin\ntest\ntest\nyou@example.com\nyou@example.com" | python3 GeoHealthCheck/models.py create
+        pixi run -e dev setup
+        echo -e "admin\ntest\ntest\nyou@example.com\nyou@example.com" | pixi run -e dev python3 GeoHealthCheck/models.py create
 
     - name: Flake8 - Verify Coding Conventions ⚙️
-      run: flake8
+      run: pixi run -e dev flake8
 
     - name: Load Fixtures Test Data ⚙️
-      run: python3 GeoHealthCheck/models.py load tests/data/fixtures.json y
+      run: pixi run -e dev python3 GeoHealthCheck/models.py load tests/data/fixtures.json y
 
     - name: Run Probes ⚙️
-      run: python3 GeoHealthCheck/healthcheck.py
+      run: pixi run -e dev python3 GeoHealthCheck/healthcheck.py
 
     - name: Run Unit Tests ⚙️
-      run: python3 tests/run_tests.py
+      run: pixi run -e dev test
+
+    - name: Publish Test Report 📄
+      if: always()
+      run: cat report.md >> "$GITHUB_STEP_SUMMARY" || true
 
     - name: Build Docs 📖
-      run: cd docs && make html
+      run: pixi run -e dev bash -c "cd docs && make html"
 
     - name: Cleanup 💯
-      run: python3 GeoHealthCheck/models.py drop
+      run: pixi run -e dev python3 GeoHealthCheck/models.py drop

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>" \
@@ -12,14 +12,16 @@ ARG TZ="Etc/UTC"
 ARG LANG="en_US.UTF-8"
 ARG ADD_DEB_PACKAGES=""
 
-# General ENV settings
+# General ENV settings.
+# DEB_PACKAGES holds only non-Python system tools: Python and all app/runtime
+# deps (incl. gunicorn/gevent, lxml, pyproj) now come from the pixi env.
+# `make` is needed at build time by `invoke setup` (docs build).
 ENV LC_ALL="en_US.UTF-8" \
 	LANG="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="locales ca-certificates make postgresql-client" \
 	ADMIN_NAME=admin \
 	ADMIN_PWD=admin \
 	ADMIN_EMAIL=admin.istrator@mydomain.com \
@@ -72,10 +74,10 @@ WSGI_WORKER_CLASS='gevent' \
 # GHC User Plugins, best be overridden via Container environment \
 GHC_USER_PLUGINS=''
 
-# Install operating system dependencies
+# Install operating system dependencies (non-Python only)
 RUN \
     apt-get update \
-    && apt-get --no-install-recommends install -y ${DEB_PACKAGES} ${DEB_BUILD_DEPS} ${ADD_DEB_PACKAGES} \
+    && apt-get --no-install-recommends install -y ${DEB_PACKAGES} ${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)"
 
@@ -87,13 +89,12 @@ COPY docker/scripts/*.sh docker/config_site.py docker/plugins /
 # Add Source Code
 COPY . /GeoHealthCheck
 
-# Install
+WORKDIR /GeoHealthCheck
+
+# Install: create the locked pixi `prod` env and bootstrap GHC
 RUN \
-	chmod a+x /*.sh && ./install.sh \
-    # Cleanup TODO: remove unused Locales and TZs \
-    && apt-get remove --purge -y ${DEB_BUILD_DEPS} \
+	chmod a+x /*.sh && /install.sh \
     && apt-get clean \
-    && apt autoremove -y  \
     && rm -rf /var/lib/apt/lists/*
 
 
@@ -102,4 +103,4 @@ VOLUME ["/GeoHealthCheck/DB/"]
 
 EXPOSE ${PORT}
 
-ENTRYPOINT /run-web.sh
+ENTRYPOINT ["/run-web.sh"]

README.md

@@ -14,11 +14,11 @@ Easiest is [to run GHC using Docker](https://github.com/geopython/GeoHealthCheck
 Below a quick overview of a manual install on Unix-based systems like Apple MacOS and Linux.
 
 ```bash
-virtualenv GeoHealthCheck && cd $_
-. bin/activate
 git clone https://github.com/geopython/GeoHealthCheck.git
 cd GeoHealthCheck
-pip3 install Invoke
+# install the environment (Python + all deps) and open a shell in it
+pixi install -e prod
+pixi shell -e prod
 # setup installation
 invoke setup
 # generate secret key
@@ -69,30 +69,50 @@ 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 invoke 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 invoke create admin admin a@a.com
 
 # run locally
-python GeoHealthCheck/app.py  
+pixi run -e prod python GeoHealthCheck/app.py
 
 ```
 
+### 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/README.md

@@ -230,12 +230,10 @@ The GHC installation is at `/GeoHealthCheck` within the Docker Container.
 # Bash into running GHC Container
 docker exec -it docker_geohealthcheck_1 bash
 
-# setup Python venv
-source /venv/bin/activate .
 cd /GeoHealthCheck/
- 
-# next can use Invoke commands e.g. DB upgrade
-invoke upgrade
+
+# next can use Invoke commands via the pixi env, e.g. DB upgrade
+pixi run -e prod invoke upgrade
 
 etc
 ```

docker/scripts/configure.sh

@@ -13,9 +13,8 @@ echo "Using DB_TYPE=${DB_TYPE}"
 # 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 invoke create -u ${ADMIN_NAME} -p ${ADMIN_PWD} -e ${ADMIN_EMAIL}
 	popd || exit 1
 }
 

docker/scripts/install.sh

@@ -1,21 +1,20 @@
 #!/bin/bash
 
-# GHC Source was added in Dockerfile, install
-# NB we use gunicorn/eventlet async workers as some Probes may take a long time
-# e.g. fetching Metadata (Caps) and testing all layers
-# Install Python packages for installation and setup
+# GHC source was added in the Dockerfile; set up the pixi environment.
+# NB we use gunicorn/gevent async workers as some Probes may take a long time
+# e.g. fetching Metadata (Caps) and testing all layers.
+set -e
 
-python3 -m venv GeoHealthCheck
-pushd /GeoHealthCheck || exit 1
+cd /GeoHealthCheck || exit 1
 
-source bin/activate
+# Create the locked `prod` environment: Python plus all app/runtime deps
+# (incl. gunicorn/gevent, lxml, pyproj, invoke) from conda-forge/PyPI.
+pixi install --locked -e prod
 
+# Bootstrap GHC itself: static JS assets, i18n .mo files, local docs, dirs.
+pixi run -e prod setup
 
-# Docker-specific deps
-pip3 install --no-cache-dir -r docker/scripts/requirements.txt
-
-# Sets up GHC itself
-invoke setup
+# Use the Docker-specific site config (overrides the default from setup).
 mv /config_site.py /GeoHealthCheck/instance/config_site.py
 
 # Copy possible Plugins into app tree
@@ -28,5 +27,3 @@ then
 	# Remove to allow later Volume mount of /plugins
 	rm -rf /plugins
 fi
-
-popd || exit 1

docker/scripts/run-runner.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 invoke runner-daemon
 
 echo "END /run-runner.sh"

docker/scripts/run-tests.sh

@@ -17,7 +17,6 @@ echo "START /run-tests.sh"
 export PYTHONPATH=/GeoHealthCheck/GeoHealthCheck:$PYTHONPATH
 
 cd /GeoHealthCheck
-source bin/activate
-invoke run-tests
+pixi run -e prod invoke run-tests
 
 echo "END /run-tests.sh"

docker/scripts/run-web.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Runs the GHC app with gunicorn
+# Runs the GHC app with gunicorn (from the pixi `prod` env)
 
 echo "START /run-web.sh"
 
@@ -10,20 +10,18 @@ echo "START /run-web.sh"
 # Configure: DB and plugins.
 /configure.sh
 
-# Make sure PYTHONPATH includes GeoHealthCheck
+# Make sure PYTHONPATH includes GeoHealthCheck (for intra-package imports)
 export PYTHONPATH=/GeoHealthCheck/GeoHealthCheck:$PYTHONPATH
 
-pushd /GeoHealthCheck || exit 1
+cd /GeoHealthCheck || exit 1
 
-source bin/activate
-
-invoke upgrade
+pixi run -e prod invoke upgrade
 
 # SCRIPT_NAME should not have value '/'
 [ "${SCRIPT_NAME}" = '/' ] && export SCRIPT_NAME="" && echo "make SCRIPT_NAME empty from /"
 
 echo "Running GHC WSGI on ${HOST}:${PORT} with ${WSGI_WORKERS} workers and SCRIPT_NAME=${SCRIPT_NAME}"
-exec gunicorn --pythonpath /GeoHealthCheck/lib/python3.12/site-packages/ --workers ${WSGI_WORKERS} \
+exec pixi run -e prod gunicorn --chdir /GeoHealthCheck --workers ${WSGI_WORKERS} \
 		--worker-class=${WSGI_WORKER_CLASS} \
 		--timeout ${WSGI_WORKER_TIMEOUT} \
 		--name="Gunicorn_GHC" \

docs/admin.rst

@@ -19,7 +19,7 @@ create db
 
 To create the database execute the following:
 
-Open a command line, (if needed activate your virtualenv), and do ::
+Open a command line, (if needed, activate the pixi environment with ``pixi shell -e prod``), and do ::
 
     python3 GeoHealthCheck/models.py create
 
@@ -28,7 +28,7 @@ drop db
 
 To delete the database execute the following, however you will loose all your information. So please ensure backup if needed:
 
-Open a command line, (if needed activate your virtualenv), and do ::
+Open a command line, (if needed, activate the pixi environment with ``pixi shell -e prod``), and do ::
 
     python3 GeoHealthCheck/models.py drop
 
@@ -75,10 +75,8 @@ a password is forgotten and somehow the email-based reset is not available nor w
 In that case, password-hashes can be created from the command-line using the Python library `passlib <https://passlib.readthedocs.io/en/stable/>`_
 within an interactive Python-shell as follows: ::
 
-	$ pip3 install passlib
-	# or in Debian/Ubuntu: apt-get install python-passlib
-
-	python3
+	# passlib is part of the pixi environment; open a Python shell in it:
+	pixi run -e prod python3
 	>>> from passlib.hash import pbkdf2_sha256
 	>>>
 	>>> hash = pbkdf2_sha256.hash("mynewpassword")
@@ -109,5 +107,5 @@ Then copy-paste the hash-string into the `password`-field of the User-record in
 Build Documentation
 -------------------
 
-Open a command line, (if needed activate your virtualenv) and move into the directory  ``GeoHealthCheck/doc/``.
+Open a command line, (if needed, activate the pixi environment with ``pixi shell -e prod``) and move into the directory  ``GeoHealthCheck/doc/``.
 In there, type ``make html`` plus ENTER and the documentation should be built locally.