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Use mamba instead of conda where possible

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This commit is contained in:
Ayaz Salikhov
2021-08-24 23:41:32 +03:00
parent c3b52b9560
commit 1fce48cd6c
17 changed files with 60 additions and 88 deletions
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18
docs/using/common.md
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@@ -161,6 +161,11 @@ 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
mamba install --quiet --yes some-package && \
mamba clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
pip install --quiet --no-cache-dir some-package && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
@@ -169,27 +174,22 @@ conda install --quiet --yes some-package && \
conda clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
mamba install --quiet --yes some-package && \
mamba 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}"
```

53
docs/using/recipes.md
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@@ -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`.

2
docs/using/selecting.md
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@@ -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`)