From 7b14917cb0e235fa8f22e0ade6b4a0b4d1053b88 Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Sat, 22 May 2021 00:11:22 +0300 Subject: [PATCH 01/11] Update packages --- all-spark-notebook/Dockerfile | 7 +++---- base-notebook/Dockerfile | 8 ++++---- datascience-notebook/Dockerfile | 6 +++--- r-notebook/Dockerfile | 9 ++++----- scipy-notebook/Dockerfile | 4 ++-- 5 files changed, 16 insertions(+), 18 deletions(-) diff --git a/all-spark-notebook/Dockerfile b/all-spark-notebook/Dockerfile index cf864edc..00d504a0 100644 --- a/all-spark-notebook/Dockerfile +++ b/all-spark-notebook/Dockerfile @@ -23,12 +23,11 @@ USER $NB_UID # R packages RUN conda install --quiet --yes \ - 'r-base=4.0.3' \ + 'r-base=4.1.0' \ 'r-ggplot2=3.3*' \ - 'r-irkernel=1.1*' \ + 'r-irkernel=1.2*' \ 'r-rcurl=1.98*' \ - 'r-sparklyr=1.6*' \ - && \ + 'r-sparklyr=1.6*' && \ conda clean --all -f -y && \ fix-permissions "${CONDA_DIR}" && \ fix-permissions "/home/${NB_USER}" diff --git a/base-notebook/Dockerfile b/base-notebook/Dockerfile index c036076d..23cf4035 100644 --- a/base-notebook/Dockerfile +++ b/base-notebook/Dockerfile @@ -26,7 +26,7 @@ USER root # Conda version ARG conda_version="4.10.1" # Miniforge installer patch version -ARG miniforge_patch_number="0" +ARG miniforge_patch_number="2" # Miniforge installer architecture ARG miniforge_arch="x86_64" # Package Manager and Python implementation to use (https://github.com/conda-forge/miniforge) @@ -39,7 +39,7 @@ ARG miniforge_version="${conda_version}-${miniforge_patch_number}" # Miniforge installer ARG miniforge_installer="${miniforge_python}-${miniforge_version}-Linux-${miniforge_arch}.sh" # Miniforge checksum -ARG miniforge_checksum="d4065b376f81b83cfef0c7316f97bb83337e4ae27eb988828363a578226e3a62" +ARG miniforge_checksum="cdc6755dba2d6ffce04ef773ff5ad3e7b9878ff05d7fb43c013db94df919669d" # Install all OS dependencies for notebook server that starts but lacks all # features (e.g., download as all possible file formats) @@ -130,9 +130,9 @@ RUN wget --quiet "https://github.com/conda-forge/miniforge/releases/download/${m # Do all this in a single RUN command to avoid duplicating all of the # files across image layers when the permissions change RUN conda install --quiet --yes \ - 'notebook=6.3.0' \ + 'notebook=6.4.0' \ 'jupyterhub=1.4.1' \ - 'jupyterlab=3.0.15' && \ + 'jupyterlab=3.0.16' && \ conda clean --all -f -y && \ npm cache clean --force && \ jupyter notebook --generate-config && \ diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile index 62ce058c..a923dcf4 100644 --- a/datascience-notebook/Dockerfile +++ b/datascience-notebook/Dockerfile @@ -54,7 +54,7 @@ USER $NB_UID # R packages including IRKernel which gets installed globally. RUN conda install --quiet --yes \ - 'r-base=4.0.3' \ + 'r-base=4.1.0' \ 'r-caret=6.0*' \ 'r-crayon=1.4*' \ 'r-devtools=2.4*' \ @@ -62,11 +62,11 @@ RUN conda install --quiet --yes \ 'r-hexbin=1.28*' \ 'r-htmltools=0.5*' \ 'r-htmlwidgets=1.5*' \ - 'r-irkernel=1.1*' \ + 'r-irkernel=1.2*' \ 'r-nycflights13=1.0*' \ 'r-randomforest=4.6*' \ 'r-rcurl=1.98*' \ - 'r-rmarkdown=2.7*' \ + 'r-rmarkdown=2.8*' \ 'r-rsqlite=2.2*' \ 'r-shiny=1.6*' \ 'r-tidyverse=1.3*' \ diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile index 5b5e7b59..a3f33603 100644 --- a/r-notebook/Dockerfile +++ b/r-notebook/Dockerfile @@ -25,7 +25,7 @@ USER $NB_UID # R packages RUN conda install --quiet --yes \ - 'r-base=4.0.3' \ + 'r-base=4.1.0' \ 'r-caret=6.*' \ 'r-crayon=1.4*' \ 'r-devtools=2.4*' \ @@ -33,18 +33,17 @@ RUN conda install --quiet --yes \ 'r-hexbin=1.28*' \ 'r-htmltools=0.5*' \ 'r-htmlwidgets=1.5*' \ - 'r-irkernel=1.1*' \ + 'r-irkernel=1.2*' \ 'r-nycflights13=1.0*' \ 'r-randomforest=4.6*' \ 'r-rcurl=1.98*' \ - 'r-rmarkdown=2.7*' \ + 'r-rmarkdown=2.8*' \ 'r-rodbc=1.3*' \ 'r-rsqlite=2.2*' \ 'r-shiny=1.6*' \ 'r-tidyverse=1.3*' \ 'unixodbc=2.3.*' \ - 'r-tidymodels=0.1*' \ - && \ + 'r-tidymodels=0.1*' && \ conda clean --all -f -y && \ fix-permissions "${CONDA_DIR}" && \ fix-permissions "/home/${NB_USER}" diff --git a/scipy-notebook/Dockerfile b/scipy-notebook/Dockerfile index bedbaa02..b94a04bd 100644 --- a/scipy-notebook/Dockerfile +++ b/scipy-notebook/Dockerfile @@ -22,7 +22,7 @@ RUN conda install --quiet --yes \ 'bottleneck=1.3.*' \ 'cloudpickle=1.6.*' \ 'cython=0.29.*' \ - 'dask=2021.4.*' \ + 'dask=2021.5.*' \ 'dill=0.3.*' \ 'h5py=3.2.*' \ 'ipywidgets=7.6.*' \ @@ -32,7 +32,7 @@ RUN conda install --quiet --yes \ 'numexpr=2.7.*' \ 'pandas=1.2.*' \ 'patsy=0.5.*' \ - 'protobuf=3.15.*' \ + 'protobuf=3.17.*' \ 'pytables=3.6.*' \ 'scikit-image=0.18.*' \ 'scikit-learn=0.24.*' \ From dc05be8ff5425e0302c9487d8bcc9e83793719bd Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Sat, 22 May 2021 13:27:19 +0300 Subject: [PATCH 02/11] Downgrade r-base --- all-spark-notebook/Dockerfile | 2 +- datascience-notebook/Dockerfile | 2 +- r-notebook/Dockerfile | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/all-spark-notebook/Dockerfile b/all-spark-notebook/Dockerfile index 00d504a0..1ff7fb5b 100644 --- a/all-spark-notebook/Dockerfile +++ b/all-spark-notebook/Dockerfile @@ -23,7 +23,7 @@ USER $NB_UID # R packages RUN conda install --quiet --yes \ - 'r-base=4.1.0' \ + 'r-base=4.0.5' \ 'r-ggplot2=3.3*' \ 'r-irkernel=1.2*' \ 'r-rcurl=1.98*' \ diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile index a923dcf4..91b2de16 100644 --- a/datascience-notebook/Dockerfile +++ b/datascience-notebook/Dockerfile @@ -54,7 +54,7 @@ USER $NB_UID # R packages including IRKernel which gets installed globally. RUN conda install --quiet --yes \ - 'r-base=4.1.0' \ + 'r-base=4.0.5' \ 'r-caret=6.0*' \ 'r-crayon=1.4*' \ 'r-devtools=2.4*' \ diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile index a3f33603..2598a060 100644 --- a/r-notebook/Dockerfile +++ b/r-notebook/Dockerfile @@ -25,7 +25,7 @@ USER $NB_UID # R packages RUN conda install --quiet --yes \ - 'r-base=4.1.0' \ + 'r-base=4.0.5' \ 'r-caret=6.*' \ 'r-crayon=1.4*' \ 'r-devtools=2.4*' \ From c9b2485f22021c9c3712f7d0b1622cc22b94839a Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Sat, 22 May 2021 13:28:26 +0300 Subject: [PATCH 03/11] Update pre-commit hooks --- .pre-commit-config.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b9bbd76e..0a610e00 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,16 +1,16 @@ --- repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v3.4.0 + rev: v4.0.1 hooks: - id: check-yaml files: .*\.(yaml|yml)$ - repo: https://github.com/hadolint/hadolint.git - rev: v2.3.0 + rev: v2.4.1 hooks: - id: hadolint-docker # FIXME: remove after https://github.com/hadolint/hadolint/issues/628 is resolved - entry: hadolint/hadolint:v2.3.0 hadolint + entry: hadolint/hadolint:v2.4.1 hadolint - repo: https://github.com/adrienverge/yamllint.git rev: v1.26.1 hooks: @@ -28,11 +28,11 @@ repos: - id: shellcheck args: ["-x"] - repo: https://gitlab.com/pycqa/flake8 - rev: 3.9.1 + rev: 3.9.2 hooks: - id: flake8 - repo: https://github.com/pre-commit/mirrors-autopep8 - rev: v1.5.6 + rev: v1.5.7 hooks: - id: autopep8 - repo: https://github.com/igorshubovych/markdownlint-cli From fb06310754be2460f7bedc05ac869d239b08ad2a Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Sat, 22 May 2021 14:43:18 +0300 Subject: [PATCH 04/11] Use altair and mamba instead of conda --- all-spark-notebook/Dockerfile | 4 ++-- docs/using/selecting.md | 2 +- pyspark-notebook/Dockerfile | 2 +- scipy-notebook/Dockerfile | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/all-spark-notebook/Dockerfile b/all-spark-notebook/Dockerfile index 1ff7fb5b..64170b8c 100644 --- a/all-spark-notebook/Dockerfile +++ b/all-spark-notebook/Dockerfile @@ -22,7 +22,7 @@ RUN apt-get update && \ USER $NB_UID # R packages -RUN conda install --quiet --yes \ +RUN mamba install --quiet --yes \ 'r-base=4.0.5' \ 'r-ggplot2=3.3*' \ 'r-irkernel=1.2*' \ @@ -33,7 +33,7 @@ RUN conda install --quiet --yes \ fix-permissions "/home/${NB_USER}" # Spylon-kernel -RUN conda install --quiet --yes 'spylon-kernel=0.4*' && \ +RUN mamba install --quiet --yes 'spylon-kernel=0.4*' && \ conda clean --all -f -y && \ python -m spylon_kernel install --sys-prefix && \ rm -rf "/home/${NB_USER}/.local" && \ diff --git a/docs/using/selecting.md b/docs/using/selecting.md index 4ed7f280..0159f5a9 100644 --- a/docs/using/selecting.md +++ b/docs/using/selecting.md @@ -96,7 +96,7 @@ and versioning strategy. [cloudpickle](https://github.com/cloudpipe/cloudpickle), [dill](https://pypi.org/project/dill/), [numba](https://numba.pydata.org/), [bokeh](https://docs.bokeh.org/en/latest/), [sqlalchemy](https://www.sqlalchemy.org/), - [hdf5](https://www.h5py.org), [vincent](https://vincent.readthedocs.io/en/latest/), + [hdf5](https://www.h5py.org), [altair](https://altair-viz.github.io), [beautifulsoup](https://www.crummy.com/software/BeautifulSoup/), [protobuf](https://developers.google.com/protocol-buffers/docs/pythontutorial), [xlrd](https://www.python-excel.org), [bottleneck](https://bottleneck.readthedocs.io/en/latest/), diff --git a/pyspark-notebook/Dockerfile b/pyspark-notebook/Dockerfile index 6c24329d..736ab9e7 100644 --- a/pyspark-notebook/Dockerfile +++ b/pyspark-notebook/Dockerfile @@ -55,7 +55,7 @@ RUN cp -p "$SPARK_HOME/conf/spark-defaults.conf.template" "$SPARK_HOME/conf/spar USER $NB_UID # Install pyarrow -RUN conda install --quiet --yes --satisfied-skip-solve \ +RUN mamba install --quiet --yes --satisfied-skip-solve \ 'pyarrow=4.0.*' && \ conda clean --all -f -y && \ fix-permissions "${CONDA_DIR}" && \ diff --git a/scipy-notebook/Dockerfile b/scipy-notebook/Dockerfile index b94a04bd..6148b8dc 100644 --- a/scipy-notebook/Dockerfile +++ b/scipy-notebook/Dockerfile @@ -16,6 +16,7 @@ USER $NB_UID # Install Python 3 packages RUN conda install --quiet --yes \ + 'altair=4.1.*' \ 'beautifulsoup4=4.9.*' \ 'conda-forge::blas=*=openblas' \ 'bokeh=2.3.*' \ @@ -41,7 +42,6 @@ RUN conda install --quiet --yes \ 'sqlalchemy=1.4.*' \ 'statsmodels=0.12.*' \ 'sympy=1.8.*' \ - 'vincent=0.4.*' \ 'widgetsnbextension=3.5.*'\ 'xlrd=2.0.*' && \ conda clean --all -f -y && \ From ad87006a01234d9a63671ffee2345af5b21cf8c8 Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Sun, 23 May 2021 22:56:52 +0300 Subject: [PATCH 05/11] Replace vincent with altair in docs --- docs/using/selecting.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/using/selecting.md b/docs/using/selecting.md index a06baef6..1f4ac157 100644 --- a/docs/using/selecting.md +++ b/docs/using/selecting.md @@ -95,7 +95,8 @@ and versioning strategy. `jupyter/scipy-notebook` includes popular packages from the scientific Python ecosystem. - Everything in `jupyter/minimal-notebook` and its ancestor images -- [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/), +- [altair](https://altair-viz.github.io), + [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/), [bokeh](https://docs.bokeh.org/en/latest/), [bottleneck](https://bottleneck.readthedocs.io/en/latest/), [cloudpickle](https://github.com/cloudpipe/cloudpickle), @@ -118,7 +119,6 @@ and versioning strategy. [sqlalchemy](https://www.sqlalchemy.org/), [statsmodel](https://www.statsmodels.org/stable/index.html), [sympy](https://www.sympy.org/en/index.html), - [vincent](https://vincent.readthedocs.io/en/latest/), [widgetsnbextension](https://ipywidgets.readthedocs.io/en/latest/user_install.html#installing-in-classic-jupyter-notebook), [xlrd](https://www.python-excel.org) packages From e4f41dd4e9d2e2d180f14c019f131e37e7fde12e Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Tue, 25 May 2021 14:02:26 +0300 Subject: [PATCH 06/11] Use mamba clean --- all-spark-notebook/Dockerfile | 4 ++-- pyspark-notebook/Dockerfile | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/all-spark-notebook/Dockerfile b/all-spark-notebook/Dockerfile index 66dca532..c3922fa8 100644 --- a/all-spark-notebook/Dockerfile +++ b/all-spark-notebook/Dockerfile @@ -28,13 +28,13 @@ RUN mamba install --quiet --yes \ 'r-irkernel=1.2*' \ 'r-rcurl=1.98*' \ 'r-sparklyr=1.6*' && \ - conda clean --all -f -y && \ + mamba clean --all -f -y && \ fix-permissions "${CONDA_DIR}" && \ fix-permissions "/home/${NB_USER}" # Spylon-kernel RUN mamba install --quiet --yes 'spylon-kernel=0.4*' && \ - conda clean --all -f -y && \ + mamba clean --all -f -y && \ python -m spylon_kernel install --sys-prefix && \ rm -rf "/home/${NB_USER}/.local" && \ fix-permissions "${CONDA_DIR}" && \ diff --git a/pyspark-notebook/Dockerfile b/pyspark-notebook/Dockerfile index 2f49e8e3..846e721b 100644 --- a/pyspark-notebook/Dockerfile +++ b/pyspark-notebook/Dockerfile @@ -57,7 +57,7 @@ USER $NB_UID # Install pyarrow RUN mamba install --quiet --yes --satisfied-skip-solve \ 'pyarrow=4.0.*' && \ - conda clean --all -f -y && \ + mamba clean --all -f -y && \ fix-permissions "${CONDA_DIR}" && \ fix-permissions "/home/${NB_USER}" From 1a0c93e5e69ef19ef7fad24cc4d9d480f7034e9e Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Sat, 29 May 2021 17:37:45 +0300 Subject: [PATCH 07/11] Update miniforge --- base-notebook/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/base-notebook/Dockerfile b/base-notebook/Dockerfile index 4c5fe045..31798c59 100644 --- a/base-notebook/Dockerfile +++ b/base-notebook/Dockerfile @@ -26,7 +26,7 @@ USER root # Conda version ARG conda_version="4.10.1" # Miniforge installer patch version -ARG miniforge_patch_number="2" +ARG miniforge_patch_number="4" # Miniforge installer architecture ARG miniforge_arch="x86_64" # Package Manager and Python implementation to use (https://github.com/conda-forge/miniforge) @@ -39,7 +39,7 @@ ARG miniforge_version="${conda_version}-${miniforge_patch_number}" # Miniforge installer ARG miniforge_installer="${miniforge_python}-${miniforge_version}-Linux-${miniforge_arch}.sh" # Miniforge checksum -ARG miniforge_checksum="cdc6755dba2d6ffce04ef773ff5ad3e7b9878ff05d7fb43c013db94df919669d" +ARG miniforge_checksum="9eb335cb559644a6e462c077ebc129af51b7329817574fb707b994dafdddf2af" # Install all OS dependencies for notebook server that starts but lacks all # features (e.g., download as all possible file formats) From ea1a3ea02b2d9fd9a5a04a762e0deccd4d11a6a0 Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Sun, 6 Jun 2021 23:44:32 +0300 Subject: [PATCH 08/11] Test commit to dismiss review --- all-spark-notebook/README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/all-spark-notebook/README.md b/all-spark-notebook/README.md index bea6f931..046a19b4 100644 --- a/all-spark-notebook/README.md +++ b/all-spark-notebook/README.md @@ -11,5 +11,4 @@ Please visit the project documentation site for help using and contributing to t others. - [Jupyter Docker Stacks on ReadTheDocs](https://jupyter-docker-stacks.readthedocs.io/en/latest/index.html) -- [Selecting an Image :: Core Stacks :: jupyter/all-spark-notebook](https://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-all-spark-notebook) - [Image Specifics :: Apache Spark](https://jupyter-docker-stacks.readthedocs.io/en/latest/using/specifics.html#apache-spark) From 14e2b08a481cf5ffbcc4256b7e600042f28149f7 Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Sun, 6 Jun 2021 23:45:15 +0300 Subject: [PATCH 09/11] Revert "Test commit to dismiss review" This reverts commit ea1a3ea02b2d9fd9a5a04a762e0deccd4d11a6a0. --- all-spark-notebook/README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/all-spark-notebook/README.md b/all-spark-notebook/README.md index 046a19b4..bea6f931 100644 --- a/all-spark-notebook/README.md +++ b/all-spark-notebook/README.md @@ -11,4 +11,5 @@ Please visit the project documentation site for help using and contributing to t others. - [Jupyter Docker Stacks on ReadTheDocs](https://jupyter-docker-stacks.readthedocs.io/en/latest/index.html) +- [Selecting an Image :: Core Stacks :: jupyter/all-spark-notebook](https://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-all-spark-notebook) - [Image Specifics :: Apache Spark](https://jupyter-docker-stacks.readthedocs.io/en/latest/using/specifics.html#apache-spark) From 4d5ce319e9c4d4b09bf09759ebecd604fe6431e0 Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Wed, 9 Jun 2021 01:04:37 +0300 Subject: [PATCH 10/11] Test commit to dismiss review --- examples/docker-compose/notebook/up.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/docker-compose/notebook/up.sh b/examples/docker-compose/notebook/up.sh index c02ed3a2..cd1d1ac3 100755 --- a/examples/docker-compose/notebook/up.sh +++ b/examples/docker-compose/notebook/up.sh @@ -53,7 +53,7 @@ if [[ "${LETSENCRYPT}" == yes || "${SECURE}" == yes ]]; then fi export PORT=${PORT:=443} else - CONFIG=notebook.yml + CONFIG="notebook.yml" export PORT=${PORT:=80} fi From 155283ae1955c24c8a6a7346c4c63eb4efb5730c Mon Sep 17 00:00:00 2001 From: Ayaz Salikhov Date: Wed, 9 Jun 2021 01:13:12 +0300 Subject: [PATCH 11/11] Revert "Test commit to dismiss review" This reverts commit 4d5ce319e9c4d4b09bf09759ebecd604fe6431e0. --- examples/docker-compose/notebook/up.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/docker-compose/notebook/up.sh b/examples/docker-compose/notebook/up.sh index cd1d1ac3..c02ed3a2 100755 --- a/examples/docker-compose/notebook/up.sh +++ b/examples/docker-compose/notebook/up.sh @@ -53,7 +53,7 @@ if [[ "${LETSENCRYPT}" == yes || "${SECURE}" == yes ]]; then fi export PORT=${PORT:=443} else - CONFIG="notebook.yml" + CONFIG=notebook.yml export PORT=${PORT:=80} fi