.gitlab-ci.yml

@@ -14,4 +14,4 @@ image_build:
   script: |
     CI_COMMIT_SHA_7=$(echo $CI_COMMIT_SHA | cut -c1-7)
     docker build --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7 .
-    docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7
+    docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7
\ No newline at end of file

.renku/metadata.yml

-'@id': https://localhost/projects/oksana.riba/AMLD%202021%20Workshop
+'@id': https://renkulab.io/projects/swissai/amld-2021-workshop
 '@type':
 - http://schema.org/Project
 - http://www.w3.org/ns/prov#Location
-http://schema.org/agent: 0.13.0
+http://schema.org/agent: 0.14.2.dev8
 http://schema.org/creator:
   '@id': mailto:oksana.riba@gmail.com
   '@type':

.renku/refs/datasets/ham10000__cancer_detection_and_classification__extracted_features

+../../datasets/e02efc81-6f6f-462b-ac6a-4f4e6d01e189/metadata.yml
\ No newline at end of file

.renku/refs/datasets/ham10000__cancer_risk_groups__extracted_features

+../../datasets/873a39af-729f-4a1d-b962-91b14e0d58a1/metadata.yml
\ No newline at end of file

.renku/refs/datasets/ham10000_workshop__cancer_detection_and_classification

+../../datasets/fed6d833-3a50-4b01-b7a4-f1af118eec99/metadata.yml
\ No newline at end of file

.renku/refs/datasets/ham10000_workshop__cancer_detection_and_classification__extracted_features

+../../datasets/2070b7e8-495a-44d0-b7bf-6bf9f0f387c2/metadata.yml
\ No newline at end of file

.renku/refs/datasets/ham10000_workshop__cancer_risk_groups

+../../datasets/1d9ca28c-79fa-45f6-9a6e-c75580447e67/metadata.yml
\ No newline at end of file

.renku/refs/datasets/ham10000_workshop__cancer_risk_groups__extracted_features

+../../datasets/7c17c9e4-7d4a-40b9-a240-520dea42aab6/metadata.yml
\ No newline at end of file

.renku/renku.ini

 [renku "interactive"]
-default_url = /lab
+default_url = /lab
\ No newline at end of file
+lfs_auto_fetch = true
+
+[renku]
+autocommit_lfs = true
+lfs_threshold = 100kb

Dockerfile

@@ -3,19 +3,35 @@
 ARG RENKU_BASE_IMAGE=renku/renkulab-py:3.7-0.7.3
 FROM ${RENKU_BASE_IMAGE}
 
+# add Visual Studio Code editor
+# ENV VSCODE_VERSION=3.8.0
+RUN curl -s https://raw.githubusercontent.com/SwissDataScienceCenter/renkulab-docker/master/scripts/install-vscode.sh | bash
+
 # Uncomment and adapt if code is to be included in the image
 # COPY src /code/src
 
 # Uncomment and adapt if your R or python packages require extra linux (ubuntu) software
 # e.g. the following installs apt-utils and vim; each pkg on its own line, all lines
 # except for the last end with backslash '\' to continue the RUN line
-#
-# USER root
-# RUN apt-get update && \
-#    apt-get install -y --no-install-recommends \
-#    apt-utils \
-#    vim
-# USER ${NB_USER}
+
+USER root
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    apt-utils \
+    bash-completion \
+    vim \
+    jq \
+    less \
+    wget \
+    curl \
+    unzip \
+    bzip2 \
+    python3-opencv && \
+    apt-get -y clean && \
+    apt-get -y autoclean  && \
+    apt-get -y autoremove
+
+USER ${NB_USER}
 
 # install the python dependencies
 COPY requirements.txt environment.yml /tmp/
@@ -27,7 +43,7 @@ RUN conda env update -q -f /tmp/environment.yml && \
 # RENKU_VERSION determines the version of the renku CLI
 # that will be used in this image. To find the latest version,
 # visit https://pypi.org/project/renku/#history.
-ARG RENKU_VERSION=0.13.0
+ARG RENKU_VERSION=0.14.2.dev8
 
 ########################################################
 # Do not edit this section and do not add anything below