From 6e1a8ddf725800fe844c8da9ebc53863f09f2d4b Mon Sep 17 00:00:00 2001 From: Abdalla Date: Wed, 6 Nov 2024 15:44:15 +0000 Subject: [PATCH 1/8] check error --- docker-bits/6_rstudio.Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/docker-bits/6_rstudio.Dockerfile b/docker-bits/6_rstudio.Dockerfile index b9a3c9239..2162d9ed2 100644 --- a/docker-bits/6_rstudio.Dockerfile +++ b/docker-bits/6_rstudio.Dockerfile @@ -9,6 +9,7 @@ RUN mkdir -p /etc/rstudio && \ ENV PATH=$PATH:/usr/lib/rstudio-server/bin + # Install some default R packages RUN mamba install --quiet --yes \ 'r-rodbc' \ From 572073af30395ac37b13e17e48f8fdca67316f2d Mon Sep 17 00:00:00 2001 From: Abdalla Date: Wed, 6 Nov 2024 19:12:09 +0000 Subject: [PATCH 2/8] match the output files --- docker-bits/6_rstudio.Dockerfile | 2 -- output/jupyterlab-cpu/Dockerfile | 42 +++++++++++++++++++++++++ output/jupyterlab-pytorch/Dockerfile | 42 +++++++++++++++++++++++++ output/jupyterlab-tensorflow/Dockerfile | 42 +++++++++++++++++++++++++ output/rstudio/Dockerfile | 1 - 5 files changed, 126 insertions(+), 3 deletions(-) diff --git a/docker-bits/6_rstudio.Dockerfile b/docker-bits/6_rstudio.Dockerfile index 2162d9ed2..96f610c90 100644 --- a/docker-bits/6_rstudio.Dockerfile +++ b/docker-bits/6_rstudio.Dockerfile @@ -9,8 +9,6 @@ RUN mkdir -p /etc/rstudio && \ ENV PATH=$PATH:/usr/lib/rstudio-server/bin - -# Install some default R packages RUN mamba install --quiet --yes \ 'r-rodbc' \ 'r-tidyverse' \ diff --git a/output/jupyterlab-cpu/Dockerfile b/output/jupyterlab-cpu/Dockerfile index 3a0d81640..cd0730b19 100644 --- a/output/jupyterlab-cpu/Dockerfile +++ b/output/jupyterlab-cpu/Dockerfile @@ -305,6 +305,48 @@ COPY jupyterlab-overrides.json /opt/conda/share/jupyter/lab/settings/overrides.j ENV DEFAULT_JUPYTER_URL=/lab ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-jupyter-notebooks +############################### +### docker-bits/6_rstudio.Dockerfile +############################### + +# Harden rstudio-server +RUN mkdir -p /etc/rstudio && \ + echo "www-frame-origin=none" >> /etc/rstudio/rserver.conf && \ + echo "www-enable-origin-check=1" >> /etc/rstudio/rserver.conf && \ + echo "www-same-site=lax" >> /etc/rstudio/rserver.conf && \ + echo "restrict-directory-view=1" >> /etc/rstudio/rsession.conf && \ + # https://github.com/rstudio/rstudio/issues/14060 + echo "rsession-ld-library-path=/opt/conda/lib" >> /etc/rstudio/rserver.conf + +ENV PATH=$PATH:/usr/lib/rstudio-server/bin + +RUN mamba install --quiet --yes \ + 'r-rodbc' \ + 'r-tidyverse' \ + 'r-arrow' \ + 'r-aws.s3' \ + 'r-catools' \ + 'r-hdf5r' \ + 'r-odbc' \ + 'r-sf' \ + 'r-e1071' \ + 'r-markdown' \ + && \ + clean-layer.sh && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +RUN python3 -m pip install \ + 'jupyter-rsession-proxy==2.2.0' \ + 'jupyter-server-proxy==4.2.0' \ + 'jupyter-shiny-proxy==1.1' && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# If using the docker bit in other Dockerfiles, this must get written over in a later layer +ENV DEFAULT_JUPYTER_URL="/rstudio" +ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-r-notebooks.git + ############################### ### docker-bits/7_remove_vulnerabilities.Dockerfile ############################### diff --git a/output/jupyterlab-pytorch/Dockerfile b/output/jupyterlab-pytorch/Dockerfile index 71744806e..0744311f7 100644 --- a/output/jupyterlab-pytorch/Dockerfile +++ b/output/jupyterlab-pytorch/Dockerfile @@ -327,6 +327,48 @@ COPY jupyterlab-overrides.json /opt/conda/share/jupyter/lab/settings/overrides.j ENV DEFAULT_JUPYTER_URL=/lab ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-jupyter-notebooks +############################### +### docker-bits/6_rstudio.Dockerfile +############################### + +# Harden rstudio-server +RUN mkdir -p /etc/rstudio && \ + echo "www-frame-origin=none" >> /etc/rstudio/rserver.conf && \ + echo "www-enable-origin-check=1" >> /etc/rstudio/rserver.conf && \ + echo "www-same-site=lax" >> /etc/rstudio/rserver.conf && \ + echo "restrict-directory-view=1" >> /etc/rstudio/rsession.conf && \ + # https://github.com/rstudio/rstudio/issues/14060 + echo "rsession-ld-library-path=/opt/conda/lib" >> /etc/rstudio/rserver.conf + +ENV PATH=$PATH:/usr/lib/rstudio-server/bin + +RUN mamba install --quiet --yes \ + 'r-rodbc' \ + 'r-tidyverse' \ + 'r-arrow' \ + 'r-aws.s3' \ + 'r-catools' \ + 'r-hdf5r' \ + 'r-odbc' \ + 'r-sf' \ + 'r-e1071' \ + 'r-markdown' \ + && \ + clean-layer.sh && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +RUN python3 -m pip install \ + 'jupyter-rsession-proxy==2.2.0' \ + 'jupyter-server-proxy==4.2.0' \ + 'jupyter-shiny-proxy==1.1' && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# If using the docker bit in other Dockerfiles, this must get written over in a later layer +ENV DEFAULT_JUPYTER_URL="/rstudio" +ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-r-notebooks.git + ############################### ### docker-bits/7_remove_vulnerabilities.Dockerfile ############################### diff --git a/output/jupyterlab-tensorflow/Dockerfile b/output/jupyterlab-tensorflow/Dockerfile index 0064d6b08..23d269ef0 100644 --- a/output/jupyterlab-tensorflow/Dockerfile +++ b/output/jupyterlab-tensorflow/Dockerfile @@ -434,6 +434,48 @@ COPY jupyterlab-overrides.json /opt/conda/share/jupyter/lab/settings/overrides.j ENV DEFAULT_JUPYTER_URL=/lab ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-jupyter-notebooks +############################### +### docker-bits/6_rstudio.Dockerfile +############################### + +# Harden rstudio-server +RUN mkdir -p /etc/rstudio && \ + echo "www-frame-origin=none" >> /etc/rstudio/rserver.conf && \ + echo "www-enable-origin-check=1" >> /etc/rstudio/rserver.conf && \ + echo "www-same-site=lax" >> /etc/rstudio/rserver.conf && \ + echo "restrict-directory-view=1" >> /etc/rstudio/rsession.conf && \ + # https://github.com/rstudio/rstudio/issues/14060 + echo "rsession-ld-library-path=/opt/conda/lib" >> /etc/rstudio/rserver.conf + +ENV PATH=$PATH:/usr/lib/rstudio-server/bin + +RUN mamba install --quiet --yes \ + 'r-rodbc' \ + 'r-tidyverse' \ + 'r-arrow' \ + 'r-aws.s3' \ + 'r-catools' \ + 'r-hdf5r' \ + 'r-odbc' \ + 'r-sf' \ + 'r-e1071' \ + 'r-markdown' \ + && \ + clean-layer.sh && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +RUN python3 -m pip install \ + 'jupyter-rsession-proxy==2.2.0' \ + 'jupyter-server-proxy==4.2.0' \ + 'jupyter-shiny-proxy==1.1' && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# If using the docker bit in other Dockerfiles, this must get written over in a later layer +ENV DEFAULT_JUPYTER_URL="/rstudio" +ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-r-notebooks.git + ############################### ### docker-bits/7_remove_vulnerabilities.Dockerfile ############################### diff --git a/output/rstudio/Dockerfile b/output/rstudio/Dockerfile index 97b45104f..7f45d0f52 100644 --- a/output/rstudio/Dockerfile +++ b/output/rstudio/Dockerfile @@ -193,7 +193,6 @@ RUN mkdir -p /etc/rstudio && \ ENV PATH=$PATH:/usr/lib/rstudio-server/bin -# Install some default R packages RUN mamba install --quiet --yes \ 'r-rodbc' \ 'r-tidyverse' \ From dbbdacd3a83203e1095233d73c59e1f25e35a751 Mon Sep 17 00:00:00 2001 From: Abdalla Date: Tue, 12 Nov 2024 14:20:39 +0000 Subject: [PATCH 3/8] Updating Mamba --- output/rstudio/Dockerfile | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/output/rstudio/Dockerfile b/output/rstudio/Dockerfile index 7f45d0f52..922f56f4e 100644 --- a/output/rstudio/Dockerfile +++ b/output/rstudio/Dockerfile @@ -29,6 +29,8 @@ RUN apt-get update --yes \ && rm -rf /var/lib/apt/lists/* \ && chmod +x /usr/bin/clean-layer.sh +RUN conda install mamba=2.0.0 + ############################### ### docker-bits/3_Kubeflow.Dockerfile ############################### @@ -193,6 +195,7 @@ RUN mkdir -p /etc/rstudio && \ ENV PATH=$PATH:/usr/lib/rstudio-server/bin +# Install some default R packages RUN mamba install --quiet --yes \ 'r-rodbc' \ 'r-tidyverse' \ @@ -283,4 +286,4 @@ RUN conda config --add channels http://jfrog-platform-artifactory.jfrog-system:8 USER $NB_USER ENTRYPOINT ["tini", "--"] -CMD ["start-custom.sh"] +CMD ["start-custom.sh"] \ No newline at end of file From d83c7a325f1c6df2746dcd34b64e38cc2d15d7a5 Mon Sep 17 00:00:00 2001 From: Abdalla Date: Tue, 12 Nov 2024 15:18:31 +0000 Subject: [PATCH 4/8] test new mamba version --- docker-bits/0_cpu.Dockerfile | 2 ++ output/jupyterlab-cpu/Dockerfile | 44 ++----------------------- output/jupyterlab-pytorch/Dockerfile | 44 ++----------------------- output/jupyterlab-tensorflow/Dockerfile | 44 ++----------------------- output/rstudio/Dockerfile | 3 +- output/sas/Dockerfile | 1 - 6 files changed, 9 insertions(+), 129 deletions(-) diff --git a/docker-bits/0_cpu.Dockerfile b/docker-bits/0_cpu.Dockerfile index a65aaf0ef..6830b4fec 100644 --- a/docker-bits/0_cpu.Dockerfile +++ b/docker-bits/0_cpu.Dockerfile @@ -18,3 +18,5 @@ RUN apt-get update --yes \ && apt-get upgrade --yes libwebp7 \ && rm -rf /var/lib/apt/lists/* \ && chmod +x /usr/bin/clean-layer.sh + +RUN conda install mamba=2.0.0 diff --git a/output/jupyterlab-cpu/Dockerfile b/output/jupyterlab-cpu/Dockerfile index cd0730b19..803f4a493 100644 --- a/output/jupyterlab-cpu/Dockerfile +++ b/output/jupyterlab-cpu/Dockerfile @@ -29,6 +29,8 @@ RUN apt-get update --yes \ && rm -rf /var/lib/apt/lists/* \ && chmod +x /usr/bin/clean-layer.sh +RUN conda install mamba=2.0.0 + ############################### ### docker-bits/3_Kubeflow.Dockerfile ############################### @@ -305,48 +307,6 @@ COPY jupyterlab-overrides.json /opt/conda/share/jupyter/lab/settings/overrides.j ENV DEFAULT_JUPYTER_URL=/lab ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-jupyter-notebooks -############################### -### docker-bits/6_rstudio.Dockerfile -############################### - -# Harden rstudio-server -RUN mkdir -p /etc/rstudio && \ - echo "www-frame-origin=none" >> /etc/rstudio/rserver.conf && \ - echo "www-enable-origin-check=1" >> /etc/rstudio/rserver.conf && \ - echo "www-same-site=lax" >> /etc/rstudio/rserver.conf && \ - echo "restrict-directory-view=1" >> /etc/rstudio/rsession.conf && \ - # https://github.com/rstudio/rstudio/issues/14060 - echo "rsession-ld-library-path=/opt/conda/lib" >> /etc/rstudio/rserver.conf - -ENV PATH=$PATH:/usr/lib/rstudio-server/bin - -RUN mamba install --quiet --yes \ - 'r-rodbc' \ - 'r-tidyverse' \ - 'r-arrow' \ - 'r-aws.s3' \ - 'r-catools' \ - 'r-hdf5r' \ - 'r-odbc' \ - 'r-sf' \ - 'r-e1071' \ - 'r-markdown' \ - && \ - clean-layer.sh && \ - fix-permissions $CONDA_DIR && \ - fix-permissions /home/$NB_USER - -RUN python3 -m pip install \ - 'jupyter-rsession-proxy==2.2.0' \ - 'jupyter-server-proxy==4.2.0' \ - 'jupyter-shiny-proxy==1.1' && \ - fix-permissions $CONDA_DIR && \ - fix-permissions /home/$NB_USER - -# If using the docker bit in other Dockerfiles, this must get written over in a later layer -ENV DEFAULT_JUPYTER_URL="/rstudio" -ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-r-notebooks.git - ############################### ### docker-bits/7_remove_vulnerabilities.Dockerfile ############################### diff --git a/output/jupyterlab-pytorch/Dockerfile b/output/jupyterlab-pytorch/Dockerfile index 0744311f7..d900a2335 100644 --- a/output/jupyterlab-pytorch/Dockerfile +++ b/output/jupyterlab-pytorch/Dockerfile @@ -29,6 +29,8 @@ RUN apt-get update --yes \ && rm -rf /var/lib/apt/lists/* \ && chmod +x /usr/bin/clean-layer.sh +RUN conda install mamba=2.0.0 + ############################### ### docker-bits/2_pytorch.Dockerfile ############################### @@ -327,48 +329,6 @@ COPY jupyterlab-overrides.json /opt/conda/share/jupyter/lab/settings/overrides.j ENV DEFAULT_JUPYTER_URL=/lab ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-jupyter-notebooks -############################### -### docker-bits/6_rstudio.Dockerfile -############################### - -# Harden rstudio-server -RUN mkdir -p /etc/rstudio && \ - echo "www-frame-origin=none" >> /etc/rstudio/rserver.conf && \ - echo "www-enable-origin-check=1" >> /etc/rstudio/rserver.conf && \ - echo "www-same-site=lax" >> /etc/rstudio/rserver.conf && \ - echo "restrict-directory-view=1" >> /etc/rstudio/rsession.conf && \ - # https://github.com/rstudio/rstudio/issues/14060 - echo "rsession-ld-library-path=/opt/conda/lib" >> /etc/rstudio/rserver.conf - -ENV PATH=$PATH:/usr/lib/rstudio-server/bin - -RUN mamba install --quiet --yes \ - 'r-rodbc' \ - 'r-tidyverse' \ - 'r-arrow' \ - 'r-aws.s3' \ - 'r-catools' \ - 'r-hdf5r' \ - 'r-odbc' \ - 'r-sf' \ - 'r-e1071' \ - 'r-markdown' \ - && \ - clean-layer.sh && \ - fix-permissions $CONDA_DIR && \ - fix-permissions /home/$NB_USER - -RUN python3 -m pip install \ - 'jupyter-rsession-proxy==2.2.0' \ - 'jupyter-server-proxy==4.2.0' \ - 'jupyter-shiny-proxy==1.1' && \ - fix-permissions $CONDA_DIR && \ - fix-permissions /home/$NB_USER - -# If using the docker bit in other Dockerfiles, this must get written over in a later layer -ENV DEFAULT_JUPYTER_URL="/rstudio" -ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-r-notebooks.git - ############################### ### docker-bits/7_remove_vulnerabilities.Dockerfile ############################### diff --git a/output/jupyterlab-tensorflow/Dockerfile b/output/jupyterlab-tensorflow/Dockerfile index 23d269ef0..18a5646e9 100644 --- a/output/jupyterlab-tensorflow/Dockerfile +++ b/output/jupyterlab-tensorflow/Dockerfile @@ -29,6 +29,8 @@ RUN apt-get update --yes \ && rm -rf /var/lib/apt/lists/* \ && chmod +x /usr/bin/clean-layer.sh +RUN conda install mamba=2.0.0 + ############################### ### docker-bits/1_CUDA-11.8.0.Dockerfile ############################### @@ -434,48 +436,6 @@ COPY jupyterlab-overrides.json /opt/conda/share/jupyter/lab/settings/overrides.j ENV DEFAULT_JUPYTER_URL=/lab ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-jupyter-notebooks -############################### -### docker-bits/6_rstudio.Dockerfile -############################### - -# Harden rstudio-server -RUN mkdir -p /etc/rstudio && \ - echo "www-frame-origin=none" >> /etc/rstudio/rserver.conf && \ - echo "www-enable-origin-check=1" >> /etc/rstudio/rserver.conf && \ - echo "www-same-site=lax" >> /etc/rstudio/rserver.conf && \ - echo "restrict-directory-view=1" >> /etc/rstudio/rsession.conf && \ - # https://github.com/rstudio/rstudio/issues/14060 - echo "rsession-ld-library-path=/opt/conda/lib" >> /etc/rstudio/rserver.conf - -ENV PATH=$PATH:/usr/lib/rstudio-server/bin - -RUN mamba install --quiet --yes \ - 'r-rodbc' \ - 'r-tidyverse' \ - 'r-arrow' \ - 'r-aws.s3' \ - 'r-catools' \ - 'r-hdf5r' \ - 'r-odbc' \ - 'r-sf' \ - 'r-e1071' \ - 'r-markdown' \ - && \ - clean-layer.sh && \ - fix-permissions $CONDA_DIR && \ - fix-permissions /home/$NB_USER - -RUN python3 -m pip install \ - 'jupyter-rsession-proxy==2.2.0' \ - 'jupyter-server-proxy==4.2.0' \ - 'jupyter-shiny-proxy==1.1' && \ - fix-permissions $CONDA_DIR && \ - fix-permissions /home/$NB_USER - -# If using the docker bit in other Dockerfiles, this must get written over in a later layer -ENV DEFAULT_JUPYTER_URL="/rstudio" -ENV GIT_EXAMPLE_NOTEBOOKS=https://github.com/StatCan/aaw-contrib-r-notebooks.git - ############################### ### docker-bits/7_remove_vulnerabilities.Dockerfile ############################### diff --git a/output/rstudio/Dockerfile b/output/rstudio/Dockerfile index 922f56f4e..ff87ad5ea 100644 --- a/output/rstudio/Dockerfile +++ b/output/rstudio/Dockerfile @@ -195,7 +195,6 @@ RUN mkdir -p /etc/rstudio && \ ENV PATH=$PATH:/usr/lib/rstudio-server/bin -# Install some default R packages RUN mamba install --quiet --yes \ 'r-rodbc' \ 'r-tidyverse' \ @@ -286,4 +285,4 @@ RUN conda config --add channels http://jfrog-platform-artifactory.jfrog-system:8 USER $NB_USER ENTRYPOINT ["tini", "--"] -CMD ["start-custom.sh"] \ No newline at end of file +CMD ["start-custom.sh"] diff --git a/output/sas/Dockerfile b/output/sas/Dockerfile index ca035455b..3806f6657 100644 --- a/output/sas/Dockerfile +++ b/output/sas/Dockerfile @@ -340,7 +340,6 @@ RUN mkdir -p /etc/rstudio && \ ENV PATH=$PATH:/usr/lib/rstudio-server/bin -# Install some default R packages RUN mamba install --quiet --yes \ 'r-rodbc' \ 'r-tidyverse' \ From 941fa717cf9aff1144fa2d9e1457954a9b878f71 Mon Sep 17 00:00:00 2001 From: Abdalla Date: Tue, 12 Nov 2024 19:57:34 +0000 Subject: [PATCH 5/8] add mamba to excluded list --- tests/general/test_packages.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/general/test_packages.py b/tests/general/test_packages.py index 574aca706..0d4b042d6 100644 --- a/tests/general/test_packages.py +++ b/tests/general/test_packages.py @@ -97,6 +97,7 @@ "pyyaml", "graphviz", "pytables", + "mamba", ] From 13f6f2a1eb3d9e63426758d8753a640c7ee95261 Mon Sep 17 00:00:00 2001 From: Abdalla Date: Wed, 13 Nov 2024 14:06:25 +0000 Subject: [PATCH 6/8] update mamba for sas image --- docker-bits/0_cpu_sas.Dockerfile | 2 ++ output/sas/Dockerfile | 2 ++ 2 files changed, 4 insertions(+) diff --git a/docker-bits/0_cpu_sas.Dockerfile b/docker-bits/0_cpu_sas.Dockerfile index d334c95a4..a7e605b21 100644 --- a/docker-bits/0_cpu_sas.Dockerfile +++ b/docker-bits/0_cpu_sas.Dockerfile @@ -24,3 +24,5 @@ RUN apt-get update --yes \ RUN pip install --force-reinstall cryptography==39.0.1 && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER + +RUN conda install mamba=2.0.0 diff --git a/output/sas/Dockerfile b/output/sas/Dockerfile index 3806f6657..01fba5649 100644 --- a/output/sas/Dockerfile +++ b/output/sas/Dockerfile @@ -30,6 +30,8 @@ RUN pip install --force-reinstall cryptography==39.0.1 && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER +RUN conda install mamba=2.0.0 + ############################### ### docker-bits/3_Kubeflow.Dockerfile ############################### From 221278d0355b2f1e1cc687d137d2189f69b34466 Mon Sep 17 00:00:00 2001 From: Abdalla Date: Wed, 13 Nov 2024 17:38:42 +0000 Subject: [PATCH 7/8] break down mamba command --- docker-bits/0_cpu.Dockerfile | 2 -- docker-bits/0_cpu_sas.Dockerfile | 2 -- docker-bits/6_rstudio.Dockerfile | 7 +++++++ tests/general/test_packages.py | 1 - 4 files changed, 7 insertions(+), 5 deletions(-) diff --git a/docker-bits/0_cpu.Dockerfile b/docker-bits/0_cpu.Dockerfile index 6830b4fec..a65aaf0ef 100644 --- a/docker-bits/0_cpu.Dockerfile +++ b/docker-bits/0_cpu.Dockerfile @@ -18,5 +18,3 @@ RUN apt-get update --yes \ && apt-get upgrade --yes libwebp7 \ && rm -rf /var/lib/apt/lists/* \ && chmod +x /usr/bin/clean-layer.sh - -RUN conda install mamba=2.0.0 diff --git a/docker-bits/0_cpu_sas.Dockerfile b/docker-bits/0_cpu_sas.Dockerfile index a7e605b21..d334c95a4 100644 --- a/docker-bits/0_cpu_sas.Dockerfile +++ b/docker-bits/0_cpu_sas.Dockerfile @@ -24,5 +24,3 @@ RUN apt-get update --yes \ RUN pip install --force-reinstall cryptography==39.0.1 && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER - -RUN conda install mamba=2.0.0 diff --git a/docker-bits/6_rstudio.Dockerfile b/docker-bits/6_rstudio.Dockerfile index 96f610c90..2feb8eeeb 100644 --- a/docker-bits/6_rstudio.Dockerfile +++ b/docker-bits/6_rstudio.Dockerfile @@ -15,6 +15,13 @@ RUN mamba install --quiet --yes \ 'r-arrow' \ 'r-aws.s3' \ 'r-catools' \ + && \ + clean-layer.sh && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# Install some default R packages +RUN mamba install --quiet --yes \ 'r-hdf5r' \ 'r-odbc' \ 'r-sf' \ diff --git a/tests/general/test_packages.py b/tests/general/test_packages.py index 0d4b042d6..574aca706 100644 --- a/tests/general/test_packages.py +++ b/tests/general/test_packages.py @@ -97,7 +97,6 @@ "pyyaml", "graphviz", "pytables", - "mamba", ] From ac8a12bb8e2287110c4ec85adc9fbb503b7c37df Mon Sep 17 00:00:00 2001 From: Abdalla Date: Wed, 13 Nov 2024 17:40:01 +0000 Subject: [PATCH 8/8] Fix output folder --- output/jupyterlab-cpu/Dockerfile | 2 -- output/jupyterlab-pytorch/Dockerfile | 2 -- output/jupyterlab-tensorflow/Dockerfile | 2 -- output/rstudio/Dockerfile | 9 +++++++-- output/sas/Dockerfile | 9 +++++++-- 5 files changed, 14 insertions(+), 10 deletions(-) diff --git a/output/jupyterlab-cpu/Dockerfile b/output/jupyterlab-cpu/Dockerfile index 2eac7476e..1074c7e1a 100644 --- a/output/jupyterlab-cpu/Dockerfile +++ b/output/jupyterlab-cpu/Dockerfile @@ -29,8 +29,6 @@ RUN apt-get update --yes \ && rm -rf /var/lib/apt/lists/* \ && chmod +x /usr/bin/clean-layer.sh -RUN conda install mamba=2.0.0 - ############################### ### docker-bits/3_Kubeflow.Dockerfile ############################### diff --git a/output/jupyterlab-pytorch/Dockerfile b/output/jupyterlab-pytorch/Dockerfile index 3f4605fdc..dbe62f87a 100644 --- a/output/jupyterlab-pytorch/Dockerfile +++ b/output/jupyterlab-pytorch/Dockerfile @@ -29,8 +29,6 @@ RUN apt-get update --yes \ && rm -rf /var/lib/apt/lists/* \ && chmod +x /usr/bin/clean-layer.sh -RUN conda install mamba=2.0.0 - ############################### ### docker-bits/2_pytorch.Dockerfile ############################### diff --git a/output/jupyterlab-tensorflow/Dockerfile b/output/jupyterlab-tensorflow/Dockerfile index 1c056ef66..ecb0f5099 100644 --- a/output/jupyterlab-tensorflow/Dockerfile +++ b/output/jupyterlab-tensorflow/Dockerfile @@ -29,8 +29,6 @@ RUN apt-get update --yes \ && rm -rf /var/lib/apt/lists/* \ && chmod +x /usr/bin/clean-layer.sh -RUN conda install mamba=2.0.0 - ############################### ### docker-bits/1_CUDA-11.8.0.Dockerfile ############################### diff --git a/output/rstudio/Dockerfile b/output/rstudio/Dockerfile index b6429ecce..eb1f10b3c 100644 --- a/output/rstudio/Dockerfile +++ b/output/rstudio/Dockerfile @@ -29,8 +29,6 @@ RUN apt-get update --yes \ && rm -rf /var/lib/apt/lists/* \ && chmod +x /usr/bin/clean-layer.sh -RUN conda install mamba=2.0.0 - ############################### ### docker-bits/3_Kubeflow.Dockerfile ############################### @@ -203,6 +201,13 @@ RUN mamba install --quiet --yes \ 'r-arrow' \ 'r-aws.s3' \ 'r-catools' \ + && \ + clean-layer.sh && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# Install some default R packages +RUN mamba install --quiet --yes \ 'r-hdf5r' \ 'r-odbc' \ 'r-sf' \ diff --git a/output/sas/Dockerfile b/output/sas/Dockerfile index a9e8dd1b7..1c874feb3 100644 --- a/output/sas/Dockerfile +++ b/output/sas/Dockerfile @@ -30,8 +30,6 @@ RUN pip install --force-reinstall cryptography==39.0.1 && \ fix-permissions $CONDA_DIR && \ fix-permissions /home/$NB_USER -RUN conda install mamba=2.0.0 - ############################### ### docker-bits/3_Kubeflow.Dockerfile ############################### @@ -351,6 +349,13 @@ RUN mamba install --quiet --yes \ 'r-arrow' \ 'r-aws.s3' \ 'r-catools' \ + && \ + clean-layer.sh && \ + fix-permissions $CONDA_DIR && \ + fix-permissions /home/$NB_USER + +# Install some default R packages +RUN mamba install --quiet --yes \ 'r-hdf5r' \ 'r-odbc' \ 'r-sf' \