Maintenance sprint 26q1

.github/workflows/docker-publish.yml

@@ -6,19 +6,46 @@ on:
       - '*'
     tags:
       - '[0-9]+.[0-9]+.[0-9]+'
-  pull_request:
 
+permissions:
+  contents: read
 jobs:
   publish:
 
     runs-on: ubuntu-24.04
 
     steps:
-      - uses: actions/checkout@master
-      - name: Publish to Registry
-        uses: docker/build-push-action@v1
+      - uses: actions/checkout@61b9e3751b92087fd0b06925ba6dd6314e06f089 # master
+        with:
+          persist-credentials: false
+      - name: Log in to Docker Hub
+        uses: docker/login-action@4907a6ddec9925e35a0a9e82d7399ccc52663121 # v4.1.0
         with:
           username: ${{ secrets.pcicdevops_at_dockerhub_username }}
           password: ${{ secrets.pcicdevops_at_dockerhub_password }}
-          repository: pcic/geospatial-python
-          tag_with_ref: true
+
+      - name: Publish to Registry
+        uses: docker/build-push-action@d08e5c354a6adb9ed34480a06d141179aa583294 # v7.0.0
+        with:
+          push: true
+          tags: |
+            pcic/geospatial-python:${{ github.ref_name }}
+            ${{ github.ref_name == 'master' && 'pcic/geospatial-python:latest' || '' }}
+
+  smoke-test:
+    needs: publish
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@61b9e3751b92087fd0b06925ba6dd6314e06f089 # master
+        with:
+          persist-credentials: false
+
+      - name: Pull the published image
+        run: docker pull pcic/geospatial-python:${{ github.ref_name }}
+
+      - name: Verify each library imports and reports a version
+        run: |
+          docker run --rm \
+            -v "$PWD/ci:/ci:ro" \
+            pcic/geospatial-python:${{ github.ref_name }} \
+            python3 /ci/smoke_test.py

.gitignore

@@ -0,0 +1,220 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+*.lcov
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+# Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi/*
+!.pixi/config.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule*
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+# .idea/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+# Temporary file for partial code execution
+tempCodeRunnerFile.py
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml

Dockerfile

@@ -1,23 +1,77 @@
-FROM ubuntu:24.04
+# syntax=docker/dockerfile:1
 
-LABEL Maintainer="James Hiebert <hiebert@uvic.ca>"
+# Ubuntu 26.04 LTS ships Python 3.14 and GDAL 3.12 as distro defaults, so the
+# GDAL Python bindings (built from source against libgdal-dev) match the system
+# library exactly. The build is split into two stages: a build stage with the
+# compilers and -dev headers needed to compile the C extensions, and a slim
+# runtime stage that carries only the shared libraries they link against.
+
+############################
+# Build stage
+############################
+FROM ubuntu:26.04 AS build
+
+LABEL org.opencontainers.image.authors="James Hiebert <hiebert@uvic.ca>"
 
 ARG DEBIAN_FRONTEND=noninteractive
+ENV PIP_NO_CACHE_DIR=1 \
+    PIP_DISABLE_PIP_VERSION_CHECK=1
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        python3 \
+        python3-dev \
+        python3-venv \
+        g++ \
+        libgdal-dev \
+        libhdf5-dev \
+        libnetcdf-dev \
+        libyaml-dev \
+        libpq-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Build into an isolated virtualenv instead of the system interpreter; this
+# avoids pip's --break-system-packages 
+RUN python3 -m venv /opt/venv
+ENV PATH="/opt/venv/bin:$PATH" \
+    VIRTUAL_ENV="/opt/venv"
 
-RUN apt-get update && apt-get install -yq \
-    libhdf5-dev \
-    libnetcdf-dev \
-    libyaml-dev \
-    libgdal-dev \
-    python3 \
-    python3-dev \
-    python3-pip \
-    cython3 && \
-    rm -rf /var/lib/apt/lists/*
+# numpy must be present before GDAL so the gdal_array bindings are built with
+# numpy support. The GDAL binding version is pinned to whatever libgdal-dev the
+# distro provides, so the two can never drift apart.
+RUN pip install numpy
+RUN pip install \
+        "gdal==$(gdal-config --version)" \
+        h5py \
+        netCDF4 \
+        psycopg2 \
+        PyYAML \
+        pillow
+
+############################
+# Runtime stage
+############################
+FROM ubuntu:26.04 AS runtime
+
+LABEL org.opencontainers.image.authors="James Hiebert <hiebert@uvic.ca>" \
+      org.opencontainers.image.title="geospatial-python" \
+      org.opencontainers.image.description="Ubuntu + Python base image for geospatial netCDF data and web apps" \
+      org.opencontainers.image.source="https://github.com/pacificclimate/docker-geospatial-python"
+
+ARG DEBIAN_FRONTEND=noninteractive
 
-ENV CPLUS_INCLUDE_PATH=/usr/include/gdal
-ENV C_INCLUDE_PATH=/usr/include/gdal
+# Only the shared runtime libraries the compiled extensions link against
+# (libgdal38 pulls in PROJ, GEOS, etc. on its own). No compilers or headers.
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        python3 \
+        libgdal38 \
+        libhdf5-310 \
+        libnetcdf22 \
+        libpq5 \
+        libyaml-0-2 \
+    && rm -rf /var/lib/apt/lists/*
 
-RUN pip install numpy --break-system-packages
+COPY --from=build /opt/venv /opt/venv
 
-RUN pip install gdal==3.8.4 h5py netCDF4 psycopg2 PyYAML pillow --break-system-packages
+ENV PATH="/opt/venv/bin:$PATH" \
+    VIRTUAL_ENV="/opt/venv" \
+    PYTHONUNBUFFERED=1