Revised docker setup workflow.

.gitlab-ci.yml

@@ -17,8 +17,8 @@ stages:
 test_geoarray:
   stage: test
   script:
-    - source /root/anaconda3/bin/activate
-    - export GDAL_DATA=/root/anaconda3/share/gdal
+    - source /root/miniconda3/bin/activate
+    - export GDAL_DATA=/root/miniconda3/share/gdal
     - export PYTHONPATH=$PYTHONPATH:/root  # /root <- directory needed later
     - export LD_LIBRARY_PATH=/root/anaconda3/lib:$LD_LIBRARY_PATH # /root <- directory needed later
     # update in-house dependencies
@@ -38,8 +38,8 @@ test_geoarray:
 test_styles:
   stage: test
   script:
-    - source /root/anaconda3/bin/activate
-    - export GDAL_DATA=/root/anaconda3/share/gdal
+    - source /root/miniconda3/bin/activate
+    - export GDAL_DATA=/root/miniconda3/share/gdal
     - export PYTHONPATH=$PYTHONPATH:/root  # /root <- directory needed later
     - make lint
   artifacts:
@@ -53,8 +53,8 @@ test_styles:
 test_geoarray_install:
   stage: test
   script:
-    - source /root/anaconda3/bin/activate
-    - export GDAL_DATA=/root/anaconda3/share/gdal
+    - source /root/miniconda3/bin/activate
+    - export GDAL_DATA=/root/miniconda3/share/gdal
     - conda create -y -q --name geoarray python=3
     - source activate geoarray
      # resolve some requirements with conda
@@ -106,7 +106,7 @@ deploy_pypi:
   dependencies:
     - test_geoarray
   script:   # Configure the PyPI credentials, then push the package, and cleanup the creds.
-    - source /root/anaconda3/bin/activate
+    - source /root/miniconda3/bin/activate
     - printf "[distutils]\nindex-servers =\n    pypi\n\n" >> ~/.pypirc
     - printf "[pypi]\n""repository:"" https://upload.pypi.org/legacy/\n" >> ~/.pypirc
     - printf "username= ${PYPI_USER}\n" >> ~/.pypirc

tests/CI_docker/build_testsuite_image.sh

@@ -2,7 +2,7 @@
 
 context_dir="./context"
 dockerfile="geoarray_ci.docker"
-tag="geoarray_ci:0.6.16"
+tag="geoarray_ci:0.6.17"
 gitlab_runner="geoarray_gitlab_CI_runner"
 
 echo "#### Build runner docker image"

tests/CI_docker/context/environment_geoarray.yml

+name: geoarray
+
+channels: &id1
+  - http://conda.anaconda.org/ioam  # only for holoviews
+  - http://conda.anaconda.org/conda-forge
+
+dependencies:
+  - python=3.*.*
+  - pyqt
+  - numpy
+  - gdal
+  - scikit-image
+  - rasterio
+  - pyproj
+  - lxml
+  - geopandas
+  - ipython
+  - matplotlib
+  - basemap
+  - shapely
+  - holoviews
+  - bokeh
+  - pip:
+    - dicttoxml
+    - jsmin
+    - cerberus
+    - pyprind
+    - pint
+    - iso8601
+    - tqdm
+    - mpld3
+    - sphinx-argparse
+    - six
+    - spectral
+    - flake8
+    - pycodestyle
+    - pylint
+    - pydocstyle
+    - nose
+    - nose2
+    - nose-htmloutput
+    - coverage
+    - rednose
+    - py_tools_ds>=0.10.0
+    - pandas
+    - dill
+    - mpld3
+    - geojson
+    - folium

tests/CI_docker/context/geoarray_ci.docker

-FROM centos:7
-RUN yum update -y && \
-    yum install -y wget vim bzip2 gcc gcc-c++ make libgl1-mesa-glx mesa-libGL qt5-qtbase-gui git python-devel gdb
-
-ENV anaconda_dl 'Anaconda3-5.0.0-Linux-x86_64.sh'
-RUN /bin/bash -i -c "cd /root; wget https://repo.continuum.io/archive/$anaconda_dl ; \
-    bash -i /root/$anaconda_dl -b ; \
-    rm -f /root/$anaconda_dl"
-
-# 'conda install --yes -c conda-forge 'icu=58.*' lxml' fixing a bug for conda-forge gdal build, as of 06/2017
-RUN /bin/bash -i -c "source /root/anaconda3/bin/activate ; \
-    conda install --yes pyqt ; \
-    conda install --yes -c ioam holoviews bokeh ; \
-    conda install --yes -c conda-forge numpy gdal scikit-image matplotlib rasterio pyproj basemap shapely geopandas; \
-    conda install --yes -c conda-forge 'icu=58.*' lxml ; \
-    pip install pandas dill dicttoxml jsmin cerberus pyprind pint iso8601 tqdm mpld3 sphinx-argparse \
-        folium geojson py_tools_ds>=0.9.0 flake8 pycodestyle pylint pydocstyle nose nose2 nose-htmloutput coverage \
-        rednose"
+FROM gms_base_centos:pinned_v0.1
 
 # copy some needed stuff to /root
-#COPY *.pkl /root/ # EXAMPLE
-#COPY *.h5 /root/  # EXAMPLE
-
-# install git lfs
-RUN /bin/bash -i -c "curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.rpm.sh | bash"
-
-# installing git large file support, see here: https://git-lfs.github.com/ , change version number below for future upgrades
-ENV git_lfs_v='2.1.1'
-RUN /bin/bash -i -c "wget https://github.com/git-lfs/git-lfs/releases/download/v${git_lfs_v}/git-lfs-linux-amd64-${git_lfs_v}.tar.gz; \
-    tar -zxvf git-lfs-linux-amd64-${git_lfs_v}.tar.gz; \
-    cd git-lfs-${git_lfs_v}; \
-    bash ./install.sh"
+COPY *.yml /root/
 
-# set matplotlib backend to Agg as default, Qt won't work in headless docker containers
-RUN bash -i -c 'source /root/anaconda3/bin/activate; \
-    sed -i "/backend      : tkagg/c\backend      : Agg" $(python -c "import matplotlib; print(matplotlib.matplotlib_fname())"); \
-    sed -i "/backend      : Qt4Agg/c\backend      : Agg" $(python -c "import matplotlib; print(matplotlib.matplotlib_fname())"); \
-    sed -i "/backend      : qt5agg/c\backend      : Agg" $(python -c "import matplotlib; print(matplotlib.matplotlib_fname())")'
+RUN /bin/bash -i -c "\
+    source /root/miniconda3/bin/activate ; \
+    conda env update -n root -f /root/environment_geoarray.yml"