diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..028c9ff --- /dev/null +++ b/Dockerfile @@ -0,0 +1,107 @@ + +ARG CLIMADA_VERSION=v4.0.0 +ARG PETALS_VERSION=v4.0.1 + +FROM python:3.11-slim as base-slim + +ENV APP_ROOT=/src + +WORKDIR ${APP_ROOT} + +RUN echo 'Europe/Zurich' > /etc/timezone && \ + ln -sfn /usr/share/zoneinfo/Europe/Zurich /etc/localtime + +FROM base-slim as geospatial-extras + +ENV SUMMARY="climada-container base image with installed geospatial Debian dependencies" + +RUN apt-get update \ + && apt-get install -y --no-install-recommends \ + build-essential \ + libgdal-dev \ + libgeos-dev \ + libaec-dev \ + libeccodes-dev \ + && apt-get clean \ + && apt-get autoremove -y \ + && rm -rf /var/lib/apt/lists/* + + +FROM geospatial-extras AS prep + +# Cache shapefiles for Cartopy for containers without internet access +RUN apt-get update && apt-get install -y --no-install-recommends unzip wget git +ARG SHAPEFILE_URL=https://naturalearth.s3.amazonaws.com +ARG BASE_PATH=cartopy-data/shapefiles/natural_earth +ARG NE_CULTURAL=$BASE_PATH/cultural +ARG NE_PHYSICAL=$BASE_PATH/physical +ARG TMP_FOLDER=tmp +RUN mkdir -p "$NE_CULTURAL" "$NE_PHYSICAL" + +# Download and prepare shapefiles for countries +RUN wget $SHAPEFILE_URL/10m_cultural/ne_10m_admin_0_boundary_lines_land.zip -P $TMP_FOLDER \ + && unzip $TMP_FOLDER/ne_10m_admin_0_boundary_lines_land.zip -d ${NE_CULTURAL} +RUN wget $SHAPEFILE_URL/10m_cultural/ne_10m_admin_0_countries.zip -P $TMP_FOLDER \ + && unzip $TMP_FOLDER/ne_10m_admin_0_countries.zip -d ${NE_CULTURAL} +# Download and prepare shapefiles for states and provinces +RUN wget $SHAPEFILE_URL/10m_cultural/ne_10m_admin_1_states_provinces_lines.zip -P $TMP_FOLDER \ + && unzip $TMP_FOLDER/ne_10m_admin_1_states_provinces_lines.zip -d ${NE_CULTURAL} +# Download and prepare shapefiles for world coastlines +RUN wget $SHAPEFILE_URL/10m_physical/ne_10m_coastline.zip -P $TMP_FOLDER \ + && unzip $TMP_FOLDER/ne_10m_coastline.zip -d ${NE_PHYSICAL} +RUN dir -s +RUN echo $(ls -1 .) + +# Download versions of CLIMADA +ARG GIT_FOLDER=climada_git +ARG CLIMADA_VERSION +ARG PETALS_VERSION +ARG TMP_CLIMADA=$GIT_FOLDER/tmp_climada +ARG TMP_PETALS=$GIT_FOLDER/tmp_petals +RUN mkdir -p "$TMP_CLIMADA" "$TMP_PETALS" +RUN git clone --depth 1 --branch ${CLIMADA_VERSION} https://github.com/CLIMADA-project/climada_python.git $TMP_CLIMADA \ + && git clone --depth 1 --branch ${PETALS_VERSION} https://github.com/CLIMADA-project/climada_petals.git $TMP_PETALS + +# install poetry and install python environment +COPY pyproject.toml poetry.lock ./ + +RUN pip install --upgrade pip && \ + pip install "poetry>=1.6" + +ENV PATH="/root/.local/bin:$PATH" + +# save the specific python package versions from the poetry environment +RUN poetry export -f requirements.txt --output requirements.txt + + +FROM geospatial-extras AS climada-container-image-base + +ARG CLIMADA_VERSION +ARG PETALS_VERSION +ENV VERSION=${CLIMADA_VERSION}_${PETALS_VERSION} + +# The cartopy input is copied to the default location of data_dir, cf. cartopy.config['data_dir'] +COPY --from=prep /src/cartopy-data /src/.local/share/cartopy + +COPY --from=prep /src/requirements.txt /src/climada_container/requirements.txt +COPY --from=prep /src/climada_git/tmp_climada /src/climada_python +COPY --from=prep /src/climada_git/tmp_petals /src/climada_petals + +# the specific python package versions are installed using pip +RUN cd /src/climada_container/ \ + && pip install --no-cache-dir --no-deps --require-hashes -r requirements.txt \ + && pip install --no-cache-dir --no-deps -e ../climada_python/. \ + && pip install --no-cache-dir --no-deps -e ../climada_petals/. + +# Configure matplotlib configuration directory to be writable +ARG MATPLOTLIBDIR=/home/.config/matplotlib +RUN mkdir -p $MATPLOTLIBDIR +ENV MPLCONFIGDIR=$MATPLOTLIBDIR +RUN chgrp -R 0 $MATPLOTLIBDIR && chmod -R g=u $MATPLOTLIBDIR + +WORKDIR /src + + +FROM climada-container-image-base AS climada-container-image-prod + +CMD ["jupyter", "lab", "--ip", "0.0.0.0", "--no-browser", "--allow-root"] diff --git a/README.md b/README.md new file mode 100644 index 0000000..793c706 --- /dev/null +++ b/README.md @@ -0,0 +1,42 @@ +# Containerization of CLIMADA + +This repository documents one possible path to containerize the natural catastrophe impact model CLIMADA. + +More information about CLIMADA can be found in its two repositories: + +1. the core [climada_python](https://github.com/CLIMADA-project/climada_python) [start here] +2. the petals [climada_petals](https://github.com/CLIMADA-project/climada_petals) + +Currently, this repository contains ONE of several ways to containerize CLIMADA that is targeted to an operational and +secure environment. There are several other possibilities to do a containerization that are simpler and more useful for +other purposes. This implementation was created by [MeteoeSwiss](https://github.com/MeteoSwiss) to fulfill the following needs: +- no powerful python package manager should remain in the final docker image +- only restricted internet access will be allowed for running the container, thus save the most basic plotting layers +- reasonable container size +- dependencies are stable between several re-builds to allow a stable python environment +- dependency updates are still manageable with the same dockerfile + +This example should serve simply as a recipe to create a similar container in an operational environment. +If you have your own dependencies for an application just add them to the project.toml instead of the jupyter dependencies and recreate the poetry.lock file. + +Feedback on the usefulness of this or other containerization approaches is very welcome. +## Getting started + +This containerization was tested on Linux with Linux containers. +It currently works for a specific CLIMADA version (4.0.0 climada_python, combined with 4.0.1 climada_petals) +To build and run containers [podman](https://podman.io/) is used (also [docker](https://www.docker.com/) should work). +You can try it out on most linux systems with the following commands in a terminal: +1. 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"more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] + +[metadata] +lock-version = "2.0" +python-versions = "~3.11" +content-hash = "cf104e61a83ca9e108b1fdae277d9444a20cae2855c0d2abd85f6bc7cd234b6c" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..88e92fc --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,56 @@ +[tool.poetry] +name = "climada-container" +version = "0.1.0" +description = "" +authors = ["MeteoSwiss"] +package-mode = false + +[tool.poetry.dependencies] +python = "~3.11" + +# CLIMADA dependencies for v4.0.0 (make sure these are in the range allowed by CLIMADA!) +bottleneck= "~=1.3" +cartopy = "~=0.22.0" +cfgrib = "==0.9.9.1" # is fixed because of CLIMADA +contextily = "~=1.3" +dask = { extras = ["dataframe"], version = ">=2024.4.1" } +deprecation = "~=2.1.0" +eccodes = "~=1.6.0" # does not match CLIMADA dependency >= 2.27, < 2.28 +fiona = "==1.9.6" # not strictly a CLIMADA dependency, but a transitive dependency incompatible for version >= 1.9.6 +geopandas = "~=0.13.0" +h5py = "~=3.8.0" +matplotlib = "~=3.7.1" +netcdf4 = "~=1.6.3" +numba = "~=0.57.0" +openpyxl = "~=3.1.2" +pandas = "~=2.2.1" # not strictly a CLIMADA dependency, but a transitive dependency incompatible for version >= 2.0 +pandas-datareader = "~=0.10.0" +pathos = "~=0.3.0" +pint = "~=0.22.0" +pycountry = "~=22.3.5" +pygdal = "==3.6.2.11" # has to match the version from the geospatial-extras base image +pyproj = "~=3.4.1" +rasterio = "~=1.3.6" +scikit-image = "~=0.21.0" +scikit-learn = "~=1.3.0" +scipy = "~=1.11.0" +sparse = "~=0.14" +statsmodels = "~=0.14.0" +tables = "~=3.8.0" # pip install tables is equivalent to conda install pytables https://www.pytables.org/usersguide/installation.html +tabulate = "~=0.9.0" +tqdm = "~=4.66.0" +xarray = "~=2023.8.0" +xlsxwriter = "~=3.1.0" +xyzservices = "<2023.10.1" # temporary fix can be removed with climada_python version v4.1.1 + +# dependencies we need apart from CLIMADA dependencies +jupyterlab = ">4.0.0" +jupyter-server="==2.14.0" + +#ignore_missing_imports = true +#disallow_untyped_defs = true + + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api"