Compare revisions

73bf16c1 · 3764871a · 2001560d · 0372279a · d6838b8a · fa51c06d
--- a/.gitlab-ci.yml
+++ b/.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
\ No newline at end of file
--- a/.renku/datasets/1d9ca28c-79fa-45f6-9a6e-c75580447e67/metadata.yml
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+  - '@id': https://renkulab.io/blob/1e05b963b80367ff8d1fb106fc751724e75d6cea/data/interim/ham10000__cancer_detection_and_classification__extracted_features/MobileNet_v2_HAM10000__Cancer_Detection_And_Classification_valid_01_encoded.npy
+  - '@id': https://renkulab.io/blob/1e05b963b80367ff8d1fb106fc751724e75d6cea/data/interim/ham10000__cancer_detection_and_classification__extracted_features/MobileNet_v2_HAM10000__Cancer_Detection_And_Classification_valid_01_labels.csv
+  - '@id': https://renkulab.io/blob/1e05b963b80367ff8d1fb106fc751724e75d6cea/data/interim/ham10000__cancer_detection_and_classification__extracted_features/MobileNet_v2_HAM10000__Cancer_Detection_And_Classification_valid_02_encoded.npy
+  - '@id': https://renkulab.io/blob/1e05b963b80367ff8d1fb106fc751724e75d6cea/data/interim/ham10000__cancer_detection_and_classification__extracted_features/MobileNet_v2_HAM10000__Cancer_Detection_And_Classification_valid_02_labels.csv
+  http://schema.org/identifier:
+  - '@value': b8bb0b40-ca76-411b-95fe-ac213051972f
+  http://schema.org/isPartOf:
+  - '@id': https://renkulab.io/projects/swissai/amld-2021-workshop
+  http://schema.org/keywords: []
+  http://schema.org/name:
+  - '@value': ham10000__cancer_detection_and_classification__extracted_features
+  http://schema.org/subjectOf: []
+  http://schema.org/url:
+  - '@value': https://renkulab.io/datasets/b8bb0b40-ca76-411b-95fe-ac213051972f
+  http://www.w3.org/2000/01/rdf-schema#label:
+  - '@value': b8bb0b40-ca76-411b-95fe-ac213051972f
+  http://www.w3.org/ns/prov#atLocation:
+  - '@value': .renku/datasets/e02efc81-6f6f-462b-ac6a-4f4e6d01e189
+  http://www.w3.org/ns/prov#wasDerivedFrom:
+  - '@id': https://localhost/urls/%2F%2Frenkulab.io%2Fdatasets%2Fe02efc81-6f6f-462b-ac6a-4f4e6d01e189
+- '@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:
+  - '@value': 0.14.2.dev8
+  http://schema.org/creator:
+  - '@id': mailto:oksana.riba@gmail.com
+  http://schema.org/dateCreated:
+  - '@value': '2021-03-11T22:50:56.687846+00:00'
+  http://schema.org/name:
+  - '@value': AMLD 2021 Workshop
+  http://schema.org/schemaVersion:
+  - '@value': '8'
+  https://swissdatasciencecenter.github.io/renku-ontology#automatedTemplateUpdate:
+  - '@value': false
+  https://swissdatasciencecenter.github.io/renku-ontology#immutableTemplateFiles: []
+  https://swissdatasciencecenter.github.io/renku-ontology#templateId:
+  - '@value': python-minimal
+  https://swissdatasciencecenter.github.io/renku-ontology#templateMetadata:
+  - '@value': '{"__template_source__": "https://github.com/SwissDataScienceCenter/renku-project-template",
+      "__template_ref__": "0.1.16", "__template_id__": "python-minimal", "__namespace__":
+      "swissai", "__automated_update__": true, "__repository__": "https://renkulab.io/gitlab",
+      "__sanitized_project_name__": "amld-2021-workshop", "__project_slug__": "swissai/amld-2021-workshop",
+      "description": "Practical part for AMLD 2021 Workshop based on the original
+      work of Pawel Rosikiewicz available at Github: https://github.com/PawelRosikiewicz/SkinDiagnosticAI",
+      "name": "AMLD 2021 Workshop"}'
+  https://swissdatasciencecenter.github.io/renku-ontology#templateReference:
+  - '@value': 0.1.16
+  https://swissdatasciencecenter.github.io/renku-ontology#templateSource:
+  - '@value': https://github.com/SwissDataScienceCenter/renku-project-template
+  https://swissdatasciencecenter.github.io/renku-ontology#templateVersion:
+  - '@value': 11c74ad062891b24b5873d3036eff032eebc973a
+- '@id': mailto:oksana.riba@gmail.com
+  '@type':
+  - http://schema.org/Person
+  - http://www.w3.org/ns/prov#Person
+  http://schema.org/email:
+  - '@value': oksana.riba@gmail.com
+  http://schema.org/name:
+  - '@value': Oksana Riba Grognuz
+  http://www.w3.org/2000/01/rdf-schema#label:
+  - '@value': Oksana Riba Grognuz
--- a/.renku/datasets/fed6d833-3a50-4b01-b7a4-f1af118eec99/metadata.yml
+++ b/.renku/datasets/fed6d833-3a50-4b01-b7a4-f1af118eec99/metadata.yml
--- a/.renku/metadata.yml
+++ b/.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':

--- a/.renku/refs/datasets/ham10000__cancer_detection_and_classification__extracted_features
+++ b/.renku/refs/datasets/ham10000__cancer_detection_and_classification__extracted_features
+../../datasets/e02efc81-6f6f-462b-ac6a-4f4e6d01e189/metadata.yml
\ No newline at end of file
--- a/.renku/refs/datasets/ham10000__cancer_risk_groups__extracted_features
+++ b/.renku/refs/datasets/ham10000__cancer_risk_groups__extracted_features
+../../datasets/873a39af-729f-4a1d-b962-91b14e0d58a1/metadata.yml
\ No newline at end of file
--- a/.renku/refs/datasets/ham10000_workshop__cancer_detection_and_classification
+++ b/.renku/refs/datasets/ham10000_workshop__cancer_detection_and_classification
+../../datasets/fed6d833-3a50-4b01-b7a4-f1af118eec99/metadata.yml
\ No newline at end of file
--- a/.renku/refs/datasets/ham10000_workshop__cancer_detection_and_classification__extracted_features
+++ b/.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
--- a/.renku/refs/datasets/ham10000_workshop__cancer_risk_groups
+++ b/.renku/refs/datasets/ham10000_workshop__cancer_risk_groups
+../../datasets/1d9ca28c-79fa-45f6-9a6e-c75580447e67/metadata.yml
\ No newline at end of file
--- a/.renku/refs/datasets/ham10000_workshop__cancer_risk_groups__extracted_features
+++ b/.renku/refs/datasets/ham10000_workshop__cancer_risk_groups__extracted_features
+../../datasets/7c17c9e4-7d4a-40b9-a240-520dea42aab6/metadata.yml
\ No newline at end of file
--- a/.renku/renku.ini
+++ b/.renku/renku.ini
 [renku "interactive"]
 default_url = /lab
\ No newline at end of file
+lfs_auto_fetch = true
+[renku]
+autocommit_lfs = true
+lfs_threshold = 100kb
--- a/Dockerfile
+++ b/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
+USER root
-# RUN apt-get update && \
+RUN apt-get update && \
-#    apt-get install -y --no-install-recommends \
+    apt-get install -y --no-install-recommends \
-#    apt-utils \
+    apt-utils \
-#    vim
+    bash-completion \
-# USER ${NB_USER}
+    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

--- a/Figures_for_Jupyter_notebooks/Slide1.jpeg
+++ b/Figures_for_Jupyter_notebooks/Slide1.jpeg
--- a/Figures_for_Jupyter_notebooks/Slide10.jpeg
+++ b/Figures_for_Jupyter_notebooks/Slide10.jpeg
--- a/Figures_for_Jupyter_notebooks/Slide11.jpeg
+++ b/Figures_for_Jupyter_notebooks/Slide11.jpeg
--- a/Figures_for_Jupyter_notebooks/Slide12.jpeg
+++ b/Figures_for_Jupyter_notebooks/Slide12.jpeg
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