Update docker recipe to install from source

.circleci/config.yml

@@ -20,7 +20,7 @@ jobs:
     # Run Python 3 tests
     working_directory: /test
     docker:
-      - image: continuumio/miniconda3
+      - image: esmvalgroup/esmvaltool:development
     steps:
       - checkout
       - run:
@@ -33,14 +33,6 @@ jobs:
       - run:
           # Update/Create Conda environment and run tests
           command: |
-            . /opt/conda/etc/profile.d/conda.sh
-            mkdir /logs
-            # conda update -y conda >> /logs/conda.txt 2>&1
-            conda env update >> /logs/conda.txt 2>&1
-            conda activate esmvaltool
-            # Install r-lintr for r linter test
-            Rscript esmvaltool/install/R/setup_devutils.R > /logs/R_install.txt 2>&1
-            # Run tests
             python setup.py test --addopts '-m "not installation"'
           no_output_timeout: 20m
       - save_cache:

docker/Dockerfile

@@ -1,19 +1,17 @@
-FROM continuumio/miniconda3
+FROM esmvalgroup/esmvalcore:latest
 
-# update the conda packages
-RUN conda update -y conda pip
-
-# install development tools
-RUN apt-get update -y && apt-get install -y \
-    build-essential \
-    curl \
-    unzip
+COPY . /esmvaltool
+WORKDIR /esmvaltool
 
 # install environment packages
-RUN conda install -c conda-forge -c esmvalgroup -c birdhouse esmvaltool
+RUN apt install julia -y
+RUN conda env update --name base --file environment.yml && conda clean --all -y
+RUN pip install .
+RUN Rscript esmvaltool/install/R/setup.R
+RUN julia esmvaltool/install/Julia/setup.jl
 
 # run tests
-RUN esmvaltool -h
+RUN esmvaltool version
 
 ENTRYPOINT ["esmvaltool"]
 CMD ["-h"]

docker/Dockerfile.dev

@@ -0,0 +1,13 @@
+FROM esmvalgroup/esmvalcore:latest
+
+COPY . /esmvaltool
+WORKDIR /esmvaltool
+
+RUN conda env update -n base environment.yml
+RUN pip install .[develop]
+RUN Rscript esmvaltool/install/R/setup.R
+RUN julia esmvaltool/install/Julia/setup.jl
+
+# Clean ESMValTool
+RUN pip uninstall esmvaltool -y
+RUN rm -r /esmvaltool

environment.yml

@@ -2,12 +2,10 @@
 name: esmvaltool
 channels:
   - conda-forge
-  - esmvalgroup
 
 dependencies:
   # Python packages that cannot be installed from PyPI:
   - gdal
-  - esmvalcore>=2.0.0b9,<2.1
   - esmf
   # Non-Python dependencies
   - cdo>=1.9.7
@@ -21,3 +19,4 @@ dependencies:
   - r-base>=3.5
   - r-curl  # Dependency of lintr, but fails to compile because it cannot find libcurl installed from conda.
   - r-udunits2  # Fails to compile because it cannot find udunits2 installed from conda.
+  - libblas=3.8.0=12_openblas  # Does build 13_openblas not seem to work with R requirements

esmvaltool/install/Julia/setup.jl

@@ -5,7 +5,7 @@ if VERSION >= v"0.7.0-DEV.2005"
     using Pkg
 end
 
-ENV["PYTHON"] = string(ENV["CONDA_PREFIX"], "/bin/python")
+# ENV["PYTHON"] = string(ENV["CONDA_PREFIX"], "/bin/python")
 
 Pkg.activate(@__DIR__)
 Pkg.instantiate()