Merge pull request #1441 from mathbunnyru/asalikhov/use_mamba_everywhere

Use mamba instead of conda where possible

Author: mathbunnyru

Makefile

@@ -112,9 +112,9 @@ build-all-multi: $(foreach I, $(MULTI_IMAGES), build-multi/$(I)) $(foreach I, $(
 
 
 
-check-outdated/%: ## check the outdated conda packages in a stack and produce a report (experimental)
+check-outdated/%: ## check the outdated mamba/conda packages in a stack and produce a report (experimental)
 	@TEST_IMAGE="$(OWNER)/$(notdir $@)" pytest test/test_outdated.py
-check-outdated-all: $(foreach I, $(ALL_IMAGES), check-outdated/$(I)) ## check all the stacks for outdated conda packages
+check-outdated-all: $(foreach I, $(ALL_IMAGES), check-outdated/$(I)) ## check all the stacks for outdated packages
 
 
 

base-notebook/Dockerfile

@@ -95,8 +95,9 @@ RUN set -x && \
     # Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
     conda config --system --set auto_update_conda false && \
     conda config --system --set show_channel_urls true && \
-    if [[ "${PYTHON_VERSION}" != "default" ]]; then conda install --yes python="${PYTHON_VERSION}"; fi && \
-    conda list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
+    if [[ "${PYTHON_VERSION}" != "default" ]]; then mamba install --quiet --yes python="${PYTHON_VERSION}"; fi && \
+    mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
+    # Using conda to update all packages: https://github.com/mamba-org/mamba/issues/1092
     conda update --all --quiet --yes && \
     conda clean --all -f -y && \
     rm -rf "/home/${NB_USER}/.cache/yarn" && \
@@ -109,11 +110,11 @@ RUN set -x && \
 # Correct permissions
 # 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 \
+RUN mamba install --quiet --yes \
     'notebook' \
     'jupyterhub' \
     'jupyterlab' && \
-    conda clean --all -f -y && \
+    mamba clean --all -f -y && \
     npm cache clean --force && \
     jupyter notebook --generate-config && \
     jupyter lab clean && \

binder/README.ipynb

@@ -66,14 +66,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!which conda"
+    "!which mamba"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The user has read/write access to the root conda environment."
+    "The user has read/write access to the root mamba environment."
    ]
   },
   {
@@ -89,7 +89,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The following packages are conda-installed in the base image to support [Jupyter Notebook](https://github.com/jupyter/notebook), [JupyterLab](https://github.com/jupyterlab/jupyterlab), and their use in [JupyterHub](https://github.com/jupyterhub/jupyterhub) environments (e.g., [MyBinder](https://mybinder.org/))."
+    "The following packages are mamba-installed in the base image to support [Jupyter Notebook](https://github.com/jupyter/notebook), [JupyterLab](https://github.com/jupyterlab/jupyterlab), and their use in [JupyterHub](https://github.com/jupyterhub/jupyterhub) environments (e.g., [MyBinder](https://mybinder.org/))."
    ]
   },
   {
@@ -98,7 +98,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!conda list"
+    "!mamba list"
    ]
   },
   {

datascience-notebook/Dockerfile

@@ -54,7 +54,7 @@ RUN mkdir /etc/julia && \
 USER ${NB_UID}
 
 # R packages including IRKernel which gets installed globally.
-RUN conda install --quiet --yes \
+RUN mamba install --quiet --yes \
     'r-base' \
     'r-caret' \
     'r-crayon' \
@@ -75,7 +75,7 @@ RUN conda install --quiet --yes \
     'r-tidyverse' \
     'rpy2' \
     'unixodbc' && \
-    conda clean --all -f -y && \
+    mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 

docs/contributing/stacks.md

@@ -18,7 +18,7 @@ Feel free to follow it or pave your own path using alternative services and buil
 First, install [cookiecutter](https://github.com/cookiecutter/cookiecutter) using pip or conda:
 
 ```bash
-pip install cookiecutter  # or conda install cookiecutter
+pip install cookiecutter  # or mamba install cookiecutter
 ```
 
 Run the cookiecutter command pointing to the [jupyter/cookiecutter-docker-stacks](https://github.com/jupyter/cookiecutter-docker-stacks) project on GitHub.

docs/using/common.md

@@ -161,35 +161,35 @@ You can use either `pip`, `conda` or `mamba` to install new packages without any
 
 ```bash
 # install a package into the default (python 3.x) environment and cleanup after the installation
-pip install --quiet --no-cache-dir some-package && \
+mamba install --quiet --yes some-package && \
+    mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-conda install --quiet --yes some-package && \
-    conda clean --all -f -y && \
+pip install --quiet --no-cache-dir some-package && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-mamba install --quiet --yes some-package && \
-    mamba clean --all -f -y && \
+conda install --quiet --yes some-package && \
+    conda clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 ```
 
 ### Using alternative channels
 
 Conda is configured by default to use only the [`conda-forge`](https://anaconda.org/conda-forge) channel.
-However, alternative channels can be used either one shot by overwriting the default channel in the installation command or by configuring `conda` to use different channels.
+However, alternative channels can be used either one shot by overwriting the default channel in the installation command or by configuring `mamba` to use different channels.
 The examples below show how to use the [anaconda default channels](https://repo.anaconda.com/pkgs/main) instead of `conda-forge` to install packages.
 
 ```bash
 # using defaults channels to install a package
-conda install --channel defaults humanize
+mamba install --channel defaults humanize
 # configure conda to add default channels at the top of the list
 conda config --system --prepend channels defaults
 # install a package
-conda install --quiet --yes humanize && \
-    conda clean --all -f -y && \
+mamba install --quiet --yes humanize && \
+    mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 ```

docs/using/recipes.md

@@ -21,7 +21,7 @@ docker run -it -e GRANT_SUDO=yes --user root jupyter/minimal-notebook
 **You should only enable `sudo` if you trust the user and/or if the container is running on an isolated host.**
 See [Docker security documentation](https://docs.docker.com/engine/security/userns-remap/) for more information about running containers as `root`.
 
-## Using `pip install` or `conda install` in a Child Docker image
+## Using `mamba install` or `pip install` in a Child Docker image
 
 Create a new Dockerfile like the one shown below.
 
@@ -61,8 +61,8 @@ For conda, the Dockerfile is similar:
 FROM jupyter/datascience-notebook:33add21fab64
 # Install from requirements.txt file
 COPY --chown=${NB_UID}:${NB_GID} requirements.txt /tmp/
-RUN conda install --yes --file /tmp/requirements.txt && \
-    conda clean --all -f -y && \
+RUN mamba install --yes --file /tmp/requirements.txt && \
+    mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 ```
@@ -81,8 +81,8 @@ FROM jupyter/scipy-notebook:latest
 # Create a Python 2.x environment using conda including at least the ipython kernel
 # and the kernda utility. Add any additional packages you want available for use
 # in a Python 2 notebook to the first line here (e.g., pandas, matplotlib, etc.)
-RUN conda create --quiet --yes -p "${CONDA_DIR}/envs/python2" python=2.7 ipython ipykernel kernda && \
-    conda clean --all -f -y
+RUN mamba create --quiet --yes -p "${CONDA_DIR}/envs/python2" python=2.7 ipython ipykernel kernda && \
+    mamba clean --all -f -y
 
 USER root
 
@@ -109,17 +109,17 @@ FROM jupyter/minimal-notebook:latest
 ARG conda_env=python36
 ARG py_ver=3.6
 
-# you can add additional libraries you want conda to install by listing them below the first line and ending with "&& \"
-RUN conda create --quiet --yes -p "${CONDA_DIR}/envs/${conda_env}" python=${py_ver} ipython ipykernel && \
-    conda clean --all -f -y
+# you can add additional libraries you want mamba to install by listing them below the first line and ending with "&& \"
+RUN mamba create --quiet --yes -p "${CONDA_DIR}/envs/${conda_env}" python=${py_ver} ipython ipykernel && \
+    mamba clean --all -f -y
 
 # alternatively, you can comment out the lines above and uncomment those below
 # if you'd prefer to use a YAML file present in the docker build context
 
 # COPY --chown=${NB_UID}:${NB_GID} environment.yml "/home/${NB_USER}/tmp/"
 # RUN cd "/home/${NB_USER}/tmp/" && \
-#     conda env create -p "${CONDA_DIR}/envs/${conda_env}" -f environment.yml && \
-#     conda clean --all -f -y
+#     mamba env create -p "${CONDA_DIR}/envs/${conda_env}" -f environment.yml && \
+#     mamba clean --all -f -y
 
 
 # create Python 3.x environment and link it to jupyter
@@ -195,8 +195,8 @@ notebooks, with no conversion, adding javascript Reveal.js:
 
 ```bash
 # Add Live slideshows with RISE
-RUN conda install --quiet --yes -c damianavila82 rise && \
-    conda clean --all -f -y && \
+RUN mamba install --quiet --yes -c damianavila82 rise && \
+    mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 ```
@@ -206,12 +206,12 @@ Credit: [Paolo D.](https://github.com/pdonorio) based on
 
 ## xgboost
 
-You need to install conda's gcc for Python xgboost to work properly.
+You need to install conda-forge's gcc for Python xgboost to work properly.
 Otherwise, you'll get an exception about libgomp.so.1 missing GOMP_4.0.
 
 ```bash
-conda install --quiet --yes gcc && \
-    conda clean --all -f -y && \
+mamba install --quiet --yes gcc && \
+    mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
@@ -521,29 +521,6 @@ RUN pip install --quiet --no-cache-dir jupyter_contrib_nbextensions && \
 
 Ref: <https://github.com/jupyter/docker-stacks/issues/675>
 
-## Enable auto-sklearn notebooks
-
-Using `auto-sklearn` requires `swig`, which the other notebook images lack, so it cant be experimented with.
-Also, there is no Conda package for `auto-sklearn`.
-
-```dockerfile
-ARG BASE_CONTAINER=jupyter/scipy-notebook
-FROM jupyter/scipy-notebook:latest
-
-USER root
-
-# autosklearn requires swig, which no other image has
-RUN apt-get update --yes && \
-    apt-get install --yes --no-install-recommends swig && \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
-
-USER ${NB_UID}
-
-RUN pip install --quiet --no-cache-dir auto-sklearn && \
-    fix-permissions "${CONDA_DIR}" && \
-    fix-permissions "/home/${NB_USER}"
-```
-
 ## Enable Delta Lake in Spark notebooks
 
 Please note that the [Delta Lake](https://delta.io/) packages are only available for Spark version > `3.0`.

docs/using/selecting.md

@@ -28,7 +28,7 @@ It is the basis for all other stacks.
 - Minimally-functional Jupyter Notebook server (e.g., no LaTeX support for saving notebooks as PDFs)
 - [Miniforge](https://github.com/conda-forge/miniforge) Python 3.x in `/opt/conda` with two package managers
   - [conda](https://github.com/conda/conda): "cross-platform, language-agnostic binary package manager".
-  - [mamba](https://github.com/mamba-org/mamba): "reimplementation of the conda package manager in C++".
+  - [mamba](https://github.com/mamba-org/mamba): "reimplementation of the conda package manager in C++". We use this package manager by default when installing packages.
 - `notebook`, `jupyterhub` and `jupyterlab` packages
 - No preinstalled scientific computing packages
 - Unprivileged user `jovyan` (`uid=1000`, configurable, see options) in group `users` (`gid=100`)

examples/docker-compose/notebook/Dockerfile

@@ -12,5 +12,5 @@ USER root
 USER ${NB_UID}
 
 # Switch back to jovyan to avoid accidental container runs as root
-# Add permanent pip/conda installs, data files, other user libs here
+# Add permanent mamba/pip/conda installs, data files, other user libs here
 # e.g., RUN pip install --quiet --no-cache-dir flake8

examples/make-deploy/Dockerfile

@@ -12,5 +12,5 @@ USER root
 USER ${NB_UID}
 
 # Switch back to jovyan to avoid accidental container runs as root
-# Add permanent pip/conda installs, data files, other user libs here
+# Add permanent mamba/pip/conda installs, data files, other user libs here
 # e.g., RUN pip install --quiet --no-cache-dir flake8