Merge pull request #371 from mamba-org/update-1.5.1

Update to micromamba version 1.5.1

CHANGELOG.md

@@ -3,6 +3,13 @@
 This change log covers changes to the docker image and does not include
 [changes to the micromamba program](https://github.com/mamba-org/mamba/blob/main/CHANGELOG.md).
 
+## 5 September 2023
+
+- Updated to micromamba version 1.5.1
+- Added `/usr/local/bin/_apptainer_shell.sh` for use with
+  `apptainer shell -shell /usr/local/bin/_apptainer_shell.sh ...`
+- Added FAQ on use with `apptainer`/`singularity`
+
 ## 24 August 2023
 
 - Updated to micromamba version 1.5.0

Dockerfile

@@ -3,7 +3,7 @@ ARG BASE_IMAGE=debian:bookworm-slim
 # Mutli-stage build to keep final image small. Otherwise end up with
 # curl and openssl installed
 FROM --platform=$BUILDPLATFORM $BASE_IMAGE AS stage1
-ARG VERSION=1.5.0
+ARG VERSION=1.5.1
 
 # hadolint ignore=DL3018
 RUN if grep -q '^ID=alpine$' /etc/os-release; then \

_apptainer_shell.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+/bin/bash --rcfile /root/.bashrc -i

docs/conf.py

@@ -9,7 +9,7 @@
 project = 'micromamba-docker'
 copyright = '2023, micromamba documentation contributors'
 author = 'micromamba documentation contributors'
-release = '1.5.0'
+release = '1.5.1'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/faq.rst

@@ -101,3 +101,27 @@ If you are using the ``actions/checkout`` action, you will need to add the
 ``--user=root`` option to the ``container`` section of your GitHub Action.
 This is because the ``actions/checkout`` action creates a directory in the
 container that is owned by ``root``.
+
+How can I use a ``mambaorg/micromamba`` based image with ``apptainer``?
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are three ``apptainer``/``singularity`` sub-commands that can be used to
+execute a container:
+
+#. ``apptainer run`` will execute the entrypoint script and automatically
+   activate the ``base`` environment.
+
+#. ``apptainer exec`` does not execute the entrypoint script and therefore
+   does not automatically activate the ``base`` environment. By prepending
+   ``/usr/local/bin/_entrypoint.sh`` to the command you want to execute within
+   the container, you can activate the ``base`` environment. For example:
+
+   .. code-block:: console
+
+      apptainer exec /usr/local/bin/_entrypoint.sh micromamba info
+
+#. ``apptainer shell`` does not execute the entrypoint script and therefore
+   does not automatically activate the ``base`` environment. By supplying the
+   ``--shell /usr/local/bin/_apptainer_shell.sh`` option to ``apptainer exec``,
+   you can activate the ``base`` environment. This option can alternatively be
+   supplied via the ``APPTAINER_SHELL`` environment variable.

examples/add_micromamba/Dockerfile

@@ -1,5 +1,5 @@
 # bring in the micromamba image so we can copy files from it
-FROM mambaorg/micromamba:1.5.0 as micromamba
+FROM mambaorg/micromamba:1.5.1 as micromamba
 
 # This is the image we are going add micromaba to:
 FROM tomcat:9-jdk17-temurin-focal

examples/apt_install/Dockerfile

@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.5.0
+FROM mambaorg/micromamba:1.5.1
 
 COPY --chown=$MAMBA_USER:$MAMBA_USER env.yaml /tmp/env.yaml
 RUN micromamba install -y -n base -f /tmp/env.yaml && \

examples/cmdline_spec/Dockerfile

@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.5.0
+FROM mambaorg/micromamba:1.5.1
 RUN micromamba install -y -n base -c conda-forge \
        pyopenssl=20.0.1 \
        python=3.9.1 \

examples/generate_lock/generate_lock.sh

@@ -1,4 +1,4 @@
 docker run --rm -v "$(pwd):/tmp" \
-   mambaorg/micromamba:1.5.0 /bin/bash -c "\
+   mambaorg/micromamba:1.5.1 /bin/bash -c "\
      micromamba create --yes --name new_env --file env.yaml \
      && micromamba env export --name new_env --explicit" > env.lock

examples/install_lock/Dockerfile

@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.5.0
+FROM mambaorg/micromamba:1.5.1
 COPY --chown=$MAMBA_USER:$MAMBA_USER env.lock /tmp/env.lock
 RUN micromamba install --name base --yes --file /tmp/env.lock \
     && micromamba clean --all --yes

examples/modify_username/Dockerfile

@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.5.0
+FROM mambaorg/micromamba:1.5.1
 ARG NEW_MAMBA_USER=new-username
 ARG NEW_MAMBA_USER_ID=57440
 ARG NEW_MAMBA_USER_GID=57440

examples/multi_env/Dockerfile

@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.5.0
+FROM mambaorg/micromamba:1.5.1
 COPY --chown=$MAMBA_USER:$MAMBA_USER env1.yaml /tmp/env1.yaml
 COPY --chown=$MAMBA_USER:$MAMBA_USER env2.yaml /tmp/env2.yaml
 RUN micromamba create -y -f /tmp/env1.yaml && \

examples/new_lock/Dockerfile

@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.5.0
+FROM mambaorg/micromamba:1.5.1
 COPY --chown=$MAMBA_USER:$MAMBA_USER env.lock /tmp/env.lock
 RUN micromamba create --name my_env_name --yes --file /tmp/env.lock \
     && micromamba clean --all --yes

examples/yaml_spec/Dockerfile

@@ -1,4 +1,4 @@
-FROM mambaorg/micromamba:1.5.0
+FROM mambaorg/micromamba:1.5.1
 COPY --chown=$MAMBA_USER:$MAMBA_USER env.yaml /tmp/env.yaml
 RUN micromamba install -y -n base -f /tmp/env.yaml && \
     micromamba clean --all --yes