Merge pull request #2 from crim-ca/add-first-dockerfiles

Add first dockerfiles + .yml files

README.md

@@ -1 +1,15 @@
 # pavics-jupyter-images
+
+This repo contains the different Dockerfiles used to create the images available in JupyterHub for DACCS.
+These images will be available as image choices when starting a new instance of JupyterLab from the JupyterHub interface.
+
+All Dockerfiles (eo, nlp, etc.) are derived from the 'base' image found on the repo
+[bird-house/pavics-jupyter-base](https://github.com/bird-house/pavics-jupyter-base).
+Any packages required only for a specific image can be added to its corresponding environment.yml file.
+
+These images were first initialized with the packages listed on this
+[Confluence page](https://www.crim.ca/confluence/pages/viewpage.action?pageId=58625163).
+
+The Docker image builds can be found on Docker Hub : 
+* [eo](https://hub.docker.com/repository/docker/pavics/crim-jupyter-eo)
+* [nlp](https://hub.docker.com/repository/docker/pavics/crim-jupyter-nlp)

eo/CHANGELOG.md

@@ -12,6 +12,17 @@ Fixes:
 ------
 - ...
 
+0.1.0 (2021-02-22)
+===================
+
+Changes:
+--------
+- Updated basic Dockerfile and added basic environment.yml
+
+Fixes:
+------
+- na
+
 0.0.2 (2020-12-09)
 ===================
 

eo/Dockerfile

@@ -1,3 +1,19 @@
-FROM birdhouse/pavics-jupyter-base:0.0.2
+FROM birdhouse/pavics-jupyter-base:0.1.0
 
-RUN echo "test" > /eo-img-test
+# must update conda env as root, because of a permission error when having pip dependencies in the input yml file
+USER root
+
+COPY environment.yml /environment.yml
+
+# update env "birdy"
+# use umask 0000 so that package files for the updated environment are usable by the user for the jupyter-conda-extension
+RUN umask 0000 && conda env update -f /environment.yml
+
+# fix logged warning from GDAL sub-package when accessing Sentinel data via SAFE.ZIP
+#   only problematic here when using the 'root' conda env
+#   normal user installation with conda activation configures everything correctly
+# (https://github.com/conda-forge/gdal-feedstock/issues/83#issue-162911573)
+ENV CPL_ZIP_ENCODING=UTF-8
+
+# specify user because of problem running start-notebook.sh when being root
+USER jenkins

eo/environment.yml

@@ -0,0 +1,36 @@
+name: birdy
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - affine
+  - gdal
+  - geojson
+  - pyproj
+  - shapely
+
+  # TODO: These next packages could possibly be added to a more generic 'vision' image, from which 'eo' would be built
+  - h5py
+  - googledrivedownloader
+  - opencv
+  - pillow>=7.1
+
+  # TODO: These next packages could possibly be added to a more specific 'ML' image, built from the 'eo' image
+  - cython
+  - ddt
+  - gitdb
+  - gitpython
+  - hdf5plugin
+  - lz4
+  - pyyaml
+  - scikit-learn
+  - six
+  - tensorboardX
+  - tqdm
+  - pip:
+    # Install kornia from pypi, versions from conda are older and create conflicting errors with latest python version
+    - kornia
+    - opencv-python
+    - orion
+    - torch
+    - torchvision>=0.6

nlp/CHANGELOG.md

@@ -12,6 +12,17 @@ Fixes:
 ------
 - ...
 
+0.1.0 (2021-02-22)
+===================
+
+Changes:
+--------
+- Updated basic Dockerfile and added basic environment.yml
+
+Fixes:
+------
+- na
+
 0.0.2 (2020-12-09)
 ===================
 

nlp/Dockerfile

@@ -1,3 +1,13 @@
-FROM birdhouse/pavics-jupyter-base:0.0.2
+FROM birdhouse/pavics-jupyter-base:0.1.0
 
-RUN echo "test" > /nlp-img-test
+# must update conda env as root, because of a permission error when having pip dependencies in the input yml file
+USER root
+
+COPY environment.yml /environment.yml
+
+# update env "birdy"
+# use umask 0000 so that package files for the updated environment are usable by the user for the jupyter-conda-extension
+RUN umask 0000 && conda env update -f /environment.yml
+
+# specify user because of problem running start-notebook.sh when being root
+USER jenkins

nlp/environment.yml

@@ -0,0 +1,9 @@
+name: birdy
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - intake-esm
+  - intake-stac
+  - sat-search
+  - threddsclient