Merge pull request #3 from crim-ca/custom-tutorial-notebooks

custom notebooks are added to the image

README.md

@@ -13,3 +13,11 @@ These images were first initialized with the packages listed on this
 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)
+
+The notebooks associated to each specific image are found on this repo, on their corresponding notebook subfolder. 
+
+Also, a yaml configuration file can be found for each image, containing a list of parameters used 
+by the [deploy_data_specific_image script](https://github.com/bird-house/pavics-jupyter-base/blob/master/scheduler-jobs/deploy_data_specific_image)
+on the [bird-house/pavics-jupyter-base repo](https://github.com/bird-house/pavics-jupyter-base). 
+This script is used to download and update the image's associated notebooks that should be available on 
+the JupyterLab environment for DACCS.

eo/CHANGELOG.md

@@ -12,6 +12,18 @@ Fixes:
 ------
 - ...
 
+0.2.0 (2021-05-11)
+===================
+
+Changes:
+--------
+- Custom notebooks specific to the environment can now be added to the docker image
+- New packages added to environment (rasterio, intake-stac, sat-search)
+
+Fixes:
+------
+- na
+
 0.1.0 (2021-02-22)
 ===================
 

eo/Dockerfile

@@ -1,4 +1,4 @@
-FROM birdhouse/pavics-jupyter-base:0.1.0
+FROM birdhouse/pavics-jupyter-base:0.2.0
 
 # must update conda env as root, because of a permission error when having pip dependencies in the input yml file
 USER root
@@ -15,5 +15,7 @@ RUN umask 0000 && conda env update -f /environment.yml
 # (https://github.com/conda-forge/gdal-feedstock/issues/83#issue-162911573)
 ENV CPL_ZIP_ENCODING=UTF-8
 
+COPY notebook_config.yml /notebook_config.yml
+
 # specify user because of problem running start-notebook.sh when being root
 USER jenkins

eo/environment.yml

@@ -6,7 +6,10 @@ dependencies:
   - affine
   - gdal
   - geojson
+  - intake-stac
   - pyproj
+  - rasterio
+  - sat-search
   - shapely
 
   # TODO: These next packages could possibly be added to a more generic 'vision' image, from which 'eo' would be built
@@ -27,6 +30,8 @@ dependencies:
   - six
   - tensorboardX
   - tqdm
+  # for pip packages, include even if already in pavics-jupyter-base image, to avoid a warning problem on DockerHub
+  - pip
   - pip:
     # Install kornia from pypi, versions from conda are older and create conflicting errors with latest python version
     - kornia

eo/notebook_config.yml

@@ -0,0 +1,15 @@
+# Config file containing the list of notebooks directories to download for a specific image.
+#
+# Used in the deploy-data-specific-image script from pavics-jupyter-base.
+# More details on this config can be found on this script file :
+#   https://github.com/bird-house/pavics-jupyter-base/blob/master/scheduler-jobs/deploy_data_specific_image
+
+- repo_url: https://github.com/crim-ca/pavics-jupyter-images
+  branch: master
+  source_dir: eo/notebooks
+  dest_sub_dir: eo
+
+- repo_url: https://github.com/Ouranosinc/pavics-sdi
+  branch: master
+  source_dir: docs/source/notebooks
+  dest_sub_dir: common

eo/notebooks/eo_example.ipynb

@@ -0,0 +1,45 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "framed-intranet",
+   "metadata": {},
+   "source": [
+    "## Example notebook\n",
+    "\n",
+    "This is an example notebook just for the image's first version. \n",
+    "It is used for now to test the integration of the tutorial notebooks in JupyterHub, depending of which environment is selected. \n",
+    "Additional notebooks should be added in the future."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "imposed-serve",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

nlp/CHANGELOG.md

@@ -12,6 +12,17 @@ Fixes:
 ------
 - ...
 
+0.2.0 (2021-05-11)
+===================
+
+Changes:
+--------
+- Custom notebooks specific to the environment can now be added to the docker image
+
+Fixes:
+------
+- na
+
 0.1.0 (2021-02-22)
 ===================
 

nlp/Dockerfile

@@ -1,4 +1,4 @@
-FROM birdhouse/pavics-jupyter-base:0.1.0
+FROM birdhouse/pavics-jupyter-base:0.2.0
 
 # must update conda env as root, because of a permission error when having pip dependencies in the input yml file
 USER root
@@ -9,5 +9,8 @@ COPY environment.yml /environment.yml
 # 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
 
+COPY notebook_config.yml /notebook_config.yml
+
 # specify user because of problem running start-notebook.sh when being root
 USER jenkins
+

nlp/notebook_config.yml

@@ -0,0 +1,15 @@
+# Config file containing the list of notebooks directories to download for a specific image.
+#
+# Used in the deploy-data-specific-image script from pavics-jupyter-base.
+# More details on this config can be found on this script file :
+#   https://github.com/bird-house/pavics-jupyter-base/blob/master/scheduler-jobs/deploy_data_specific_image
+
+- repo_url: https://github.com/crim-ca/pavics-jupyter-images
+  branch: master
+  source_dir: nlp/notebooks
+  dest_sub_dir: nlp
+
+- repo_url: https://github.com/Ouranosinc/pavics-sdi
+  branch: master
+  source_dir: docs/source/notebooks
+  dest_sub_dir: common

nlp/notebooks/nlp_example.ipynb

@@ -0,0 +1,45 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "framed-intranet",
+   "metadata": {},
+   "source": [
+    "## Example notebook\n",
+    "\n",
+    "This is an example notebook just for the image's first version. \n",
+    "It is used for now to test the integration of the tutorial notebooks in JupyterHub, depending of which environment is selected. \n",
+    "Additional notebooks should be added in the future."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "imposed-serve",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}