Fix docker build for 1.2.0 (#50)

mamba-ify the previous conda-pip installation

Dockerfile

@@ -1,29 +1,31 @@
-FROM continuumio/miniconda3 as base
+FROM mambaorg/micromamba as base
 
 # The environment variable ensures that the python output is set straight
 # to the terminal without buffering it first
 ENV PYTHONUNBUFFERED 1
 
 WORKDIR /app
-RUN conda install python=3.9 -y
-RUN conda install --channel conda-forge cartopy -y
-RUN conda install --channel conda-forge esmpy && conda clean -afy
 
-COPY ./requirements_minimal.txt /app/
+COPY ./environment.yml /app 
 
-RUN pip install -r requirements_minimal.txt
-RUN apt update
-RUN apt install -y libtiff5
+RUN  micromamba install -y -n base -f environment.yml && micromamba clean -afy
 
-RUN mkdir -p /notebook_dir/writable-workspace
+ENV MAMBA_DOCKERFILE_ACTIVATE=1
+RUN python -c 'import uuid; print(uuid.uuid4())' > /tmp/my_uuid
+
+# RUN pip install -r requirements_minimal.txt
+
+USER root
+RUN mkdir -p /notebook_dir/writable-workspace && chown -R ${MAMBA_USER} /notebook_dir
 
 WORKDIR /
 
-COPY . app
+COPY --chown=${MAMBA_USER} . app
 
 WORKDIR /app
 
-RUN pip install ./
+RUN pip install --no-dependencies ./
+USER ${MAMBA_USER}
 
 EXPOSE 5006
 
@@ -40,10 +42,3 @@ ENV SHOW_HEADER=1
 ENV SHOW_MODAL=1
 
 CMD exec ./start_panel.sh
-
-FROM base as base-fr
-
-ENV LANG=fr
-ENV PREFIX=analogs-fr
-
-CMD exec ./start_panel.sh

Makefile

@@ -5,12 +5,12 @@ profile:
 	panel serve Dashboard.py --prefix analogs --autoreload --log-level=debug --admin --profiler snakeviz --static-dirs fonts=./fonts
 
 build-local:
-	docker build --target base    -t analogues-spatiaux-en:dev .
-	docker build --target base-fr -t analogues-spatiaux-fr:dev .
+	docker build --target base -t analogues-spatiaux:dev .
 
 run-local:
-	docker run -p 5006:5006 -d -e BOKEH_ALLOW_WS_ORIGIN=* analogues-spatiaux-en:dev
-	docker run -p 5007:5006 -d -e BOKEH_ALLOW_WS_ORIGIN=* analogues-spatiaux-fr:dev
+	docker rm -f analogues-spatiaux-en analogues-spatiaux-fr
+	docker run -p 5006:5006 -d -e LANG=en -e BOKEH_ALLOW_WS_ORIGIN=* --name analogues-spatiaux-en analogues-spatiaux:dev 
+	docker run -p 5007:5006 -d -e LANG=fr -e BOKEH_ALLOW_WS_ORIGIN=* --name analogues-spatiaux-fr analogues-spatiaux:dev 
 
 rm-local:
 	CONTAINER_NAME="$(shell docker ps -a -q --filter ancestor='analogues-spatiaux-en:dev' --format="{{.ID}}")";docker stop $$CONTAINER_NAME;docker rm $$CONTAINER_NAME

environment.yml

@@ -0,0 +1,29 @@
+name: analogues
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - cartopy=0.21
+  - esmpy=8.4
+  - xclim=0.44
+  - pandas=1.3
+  - panel=0.14
+  - param=1.13
+  - bokeh=2.4
+  - statsmodels
+  - numpy=1.22
+  - clisops=0.11
+  - dask=2023.8
+  - geopandas=0.13
+  - intake=0.7
+  - joblib=1.3
+  - jupyter=1.0
+  - matplotlib=3.4
+  - PyYAML=6.0
+  - Shapely=2.0
+  - xarray=2023.1
+  - xesmf=0.7
+  - geoviews=1.9
+  - hvplot=0.8
+  - pyogrio=0.6

requirements_prod.txt

@@ -0,0 +1,182 @@
+# requirements as of september 2023, kept for posterity.
+anyio==3.7.1
+appdirs==1.4.4
+argon2-cffi==23.1.0
+argon2-cffi-bindings==21.2.0
+arrow==1.2.3
+asttokens==2.2.1
+async-lru==2.0.4
+attrs==23.1.0
+Babel==2.12.1
+backcall==0.2.0
+beautifulsoup4==4.12.2
+bleach==6.0.0
+bokeh==2.4.3
+boltons==23.0.0
+Bottleneck==1.3.7
+brotlipy==0.7.0
+Cartopy==0.21.1
+certifi==2023.7.22
+cf-xarray==0.8.4
+cffi==1.15.1
+cftime==1.6.2
+charset-normalizer==2.0.4
+click==8.1.7
+click-plugins==1.1.1
+cligj==0.7.2
+clisops==0.11.0
+cloudpickle==2.2.1
+colorcet==3.0.1
+comm==0.1.4
+cryptography==39.0.1
+cycler==0.11.0
+dask==2023.8.1
+debugpy==1.6.7.post1
+decorator==5.1.1
+defusedxml==0.7.1
+distributed==2023.8.1
+entrypoints==0.4
+esmpy==8.4.2
+exceptiongroup==1.1.3
+executing==1.2.0
+fastjsonschema==2.18.0
+Fiona==1.9.4.post1
+fqdn==1.5.1
+fsspec==2023.6.0
+geopandas==0.13.2
+geoviews==1.9.6
+holoviews==1.17.1
+hvplot==0.8.4
+idna==3.4
+importlib-metadata==6.8.0
+intake==0.7.0
+ipykernel==6.25.1
+ipython==8.14.0
+ipython-genutils==0.2.0
+ipywidgets==8.1.0
+isoduration==20.11.0
+jedi==0.19.0
+Jinja2==3.1.2
+joblib==1.3.2
+json5==0.9.14
+jsonpatch==1.32
+jsonpickle==3.0.2
+jsonpointer==2.1
+jsonschema==4.19.0
+jsonschema-specifications==2023.7.1
+jupyter==1.0.0
+jupyter_client==8.3.1
+jupyter-console==6.6.3
+jupyter_core==5.3.1
+jupyter-events==0.7.0
+jupyter-lsp==2.2.0
+jupyter_server==2.7.2
+jupyter_server_terminals==0.4.4
+jupyterlab==4.0.5
+jupyterlab-pygments==0.2.2
+jupyterlab_server==2.24.0
+jupyterlab-widgets==3.0.8
+kiwisolver==1.4.4
+llvmlite==0.40.1
+lmoments3==1.0.6
+locket==1.0.0
+loguru==0.7.0
+lz4==4.3.2
+Markdown==3.4.4
+MarkupSafe==2.1.3
+matplotlib==3.4.3
+matplotlib-inline==0.1.6
+mistune==3.0.1
+msgpack==1.0.5
+nbclient==0.8.0
+nbconvert==7.8.0
+nbformat==5.9.2
+nest-asyncio==1.5.7
+netCDF4==1.6.4
+notebook==7.0.3
+notebook_shim==0.2.3
+numba==0.57.1
+numpy==1.22.3
+overrides==7.4.0
+packaging==23.0
+pandas==1.3.5
+pandocfilters==1.5.0
+panel==0.14.4
+param==1.13.0
+parso==0.8.3
+partd==1.4.0
+patsy==0.5.3
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==9.4.0
+Pint==0.22
+pip==23.2.1
+platformdirs==3.10.0
+pluggy==1.0.0
+pooch==1.7.0
+prometheus-client==0.17.1
+prompt-toolkit==3.0.39
+psutil==5.9.5
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pyarrow==13.0.0
+pycparser==2.21
+pyct==0.5.0
+Pygments==2.16.1
+pyogrio==0.6.0
+pyOpenSSL==23.2.0
+pyparsing==3.1.1
+pyproj==3.4.1
+pyshp==2.3.1
+PySocks==1.7.1
+python-dateutil==2.8.2
+python-json-logger==2.0.7
+pytz==2023.3
+pyviz_comms==3.0.0
+PyYAML==6.0.1
+pyzmq==25.1.1
+qtconsole==5.4.3
+QtPy==2.4.0
+referencing==0.30.2
+requests==2.31.0
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+roocs-utils==0.6.4
+rpds-py==0.10.0
+ruamel.yaml==0.17.21
+ruamel.yaml.clib==0.2.6
+scikit-learn==1.3.0
+scipy==1.11.2
+Send2Trash==1.8.2
+setuptools==68.0.0
+shapely==2.0.1
+six==1.16.0
+sniffio==1.3.0
+sortedcontainers==2.4.0
+soupsieve==2.4.1
+sparse==0.14.0
+stack-data==0.6.2
+statsmodels==0.14.0
+tblib==2.0.0
+terminado==0.17.1
+threadpoolctl==3.2.0
+tinycss2==1.2.1
+tomli==2.0.1
+toolz==0.12.0
+tornado==6.3.3
+tqdm==4.65.0
+traitlets==5.9.0
+typing_extensions==4.7.1
+uri-template==1.3.0
+urllib3==1.26.16
+wcwidth==0.2.6
+webcolors==1.13
+webencodings==0.5.1
+websocket-client==1.6.2
+wheel==0.38.4
+widgetsnbextension==4.0.8
+xarray==2023.1.0
+xclim==0.44.0
+xesmf==0.7.1
+zict==3.0.0
+zipp==3.16.2