Merge e4c2b41097 into d2f467cef6

[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -11,7 +11,7 @@
 repos:
   # Autoformat: Python code, syntax patterns are modernized
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.2
     hooks:
       - id: pyupgrade
         args:
@@ -23,7 +23,7 @@ repos:
 
   # Autoformat: Python code
   - repo: https://github.com/psf/black
-    rev: 24.1.1
+    rev: 24.3.0
     hooks:
       - id: black
         args:

Dockerfile

@@ -1,16 +1,21 @@
 # syntax = docker/dockerfile:1.3
-ARG ALPINE_VERSION=3.17
+ARG ALPINE_VERSION=3.19
 FROM alpine:${ALPINE_VERSION}
 
 RUN apk add --no-cache git python3 python3-dev py3-pip py3-setuptools build-base
 
-# build wheels in first image
+# build wheels in a build stage
+ARG VIRTUAL_ENV=/opt/venv
+ENV PATH=${VIRTUAL_ENV}/bin:${PATH}
+
+RUN python3 -m venv ${VIRTUAL_ENV}
+
 ADD . /tmp/src
 RUN cd /tmp/src && git clean -xfd && git status
 RUN mkdir /tmp/wheelhouse \
  && cd /tmp/wheelhouse \
- && pip3 install wheel \
- && pip3 wheel --no-cache-dir /tmp/src \
+ && pip install wheel \
+ && pip wheel --no-cache-dir /tmp/src \
  && ls -l /tmp/wheelhouse
 
 FROM alpine:${ALPINE_VERSION}
@@ -18,13 +23,18 @@ FROM alpine:${ALPINE_VERSION}
 # install python, git, bash, mercurial
 RUN apk add --no-cache git git-lfs python3 py3-pip py3-setuptools bash docker mercurial
 
+ARG VIRTUAL_ENV=/opt/venv
+ENV PATH=${VIRTUAL_ENV}/bin:${PATH}
+
+RUN python3 -m venv ${VIRTUAL_ENV}
+
 # install hg-evolve (Mercurial extensions)
-RUN pip3 install hg-evolve --user --no-cache-dir
+RUN pip install hg-evolve --no-cache-dir
 
 # install repo2docker
 COPY --from=0 /tmp/wheelhouse /tmp/wheelhouse
-RUN pip3 install --no-cache-dir --ignore-installed --no-deps /tmp/wheelhouse/*.whl \
- && pip3 list
+RUN pip install --no-cache-dir --ignore-installed --no-deps /tmp/wheelhouse/*.whl \
+ && pip list
 
 # add git-credential helper
 COPY ./docker/git-credential-env /usr/local/bin/git-credential-env

docs/source/changelog.md

@@ -1,5 +1,63 @@
 # Changelog
 
+## Version 2024.03.0
+
+([full changelog](https://github.com/jupyterhub/repo2docker/compare/2023.06.0...2024.01.03))
+
+### New features added
+
+- Implement support for dockerignore and containerignore [#1205](https://github.com/jupyterhub/repo2docker/pull/1205) ([@sgaist](https://github.com/sgaist))
+
+### Enhancements made
+
+- rstudio: log-level info to stderr [#1317](https://github.com/jupyterhub/repo2docker/pull/1317) ([@manics](https://github.com/manics))
+
+### Bugs fixed
+
+- Get Zenodo working again [#1315](https://github.com/jupyterhub/repo2docker/pull/1315) ([@manics](https://github.com/manics))
+
+### Maintenance and upkeep improvements
+
+- Update mamba to 1.5.7 from 1.5.1, and conda to 24.3.0 from 23.7.4 [#1337](https://github.com/jupyterhub/repo2docker/pull/1337) ([@SylvainCorlay](https://github.com/SylvainCorlay))
+- Dockerfile: bump alpine from 3.17 to 3.19 and Python 3.10 to 3.11 [#1332](https://github.com/jupyterhub/repo2docker/pull/1332) ([@yuvipanda](https://github.com/yuvipanda))
+- Upgrade base image from to Ubuntu 22.04 from 18.04 [#1287](https://github.com/jupyterhub/repo2docker/pull/1287) ([@yuvipanda](https://github.com/yuvipanda))
+
+### Documentation improvements
+
+- Add Ubuntu 22.04 upgrade guide [#1309](https://github.com/jupyterhub/repo2docker/pull/1309) ([@manics](https://github.com/manics))
+- Update version of R available [#1288](https://github.com/jupyterhub/repo2docker/pull/1288) ([@yuvipanda](https://github.com/yuvipanda))
+- Add changelog for 2023.06.0 [#1286](https://github.com/jupyterhub/repo2docker/pull/1286) ([@yuvipanda](https://github.com/yuvipanda))
+
+### Other merged PRs
+
+- [pre-commit.ci] pre-commit autoupdate [#1333](https://github.com/jupyterhub/repo2docker/pull/1333) ([@pre-commit-ci](https://github.com/pre-commit-ci))
+- build(deps): bump codecov/codecov-action from 3 to 4 [#1331](https://github.com/jupyterhub/repo2docker/pull/1331) ([@dependabot](https://github.com/dependabot))
+- Support pytest=8 [#1330](https://github.com/jupyterhub/repo2docker/pull/1330) ([@manics](https://github.com/manics))
+- Update versioneer [#1329](https://github.com/jupyterhub/repo2docker/pull/1329) ([@TimoRoth](https://github.com/TimoRoth))
+- build(deps): bump actions/setup-python from 4 to 5 [#1328](https://github.com/jupyterhub/repo2docker/pull/1328) ([@dependabot](https://github.com/dependabot))
+- build(deps): bump actions/upload-artifact from 3 to 4 [#1327](https://github.com/jupyterhub/repo2docker/pull/1327) ([@dependabot](https://github.com/dependabot))
+- Add NYCU Dataverse [#1326](https://github.com/jupyterhub/repo2docker/pull/1326) ([@twtw](https://github.com/twtw))
+- [pre-commit.ci] pre-commit autoupdate [#1322](https://github.com/jupyterhub/repo2docker/pull/1322) ([@pre-commit-ci](https://github.com/pre-commit-ci))
+- New domain for Edmond MPG repository [#1321](https://github.com/jupyterhub/repo2docker/pull/1321) ([@haarli](https://github.com/haarli))
+- [pre-commit.ci] pre-commit autoupdate [#1319](https://github.com/jupyterhub/repo2docker/pull/1319) ([@pre-commit-ci](https://github.com/pre-commit-ci))
+- [MRG] docs: Add base_image parameter example. [#1318](https://github.com/jupyterhub/repo2docker/pull/1318) ([@hiroyuki-sato](https://github.com/hiroyuki-sato))
+- Upgrade mamba and refreeze [#1313](https://github.com/jupyterhub/repo2docker/pull/1313) ([@manics](https://github.com/manics))
+- r: Bump version of rsession-proxy [#1310](https://github.com/jupyterhub/repo2docker/pull/1310) ([@yuvipanda](https://github.com/yuvipanda))
+- build(deps): bump actions/checkout from 3 to 4 [#1308](https://github.com/jupyterhub/repo2docker/pull/1308) ([@dependabot](https://github.com/dependabot))
+- build(deps): bump docker/build-push-action from 4 to 5 [#1307](https://github.com/jupyterhub/repo2docker/pull/1307) ([@dependabot](https://github.com/dependabot))
+- build(deps): bump docker/setup-qemu-action from 2 to 3 [#1306](https://github.com/jupyterhub/repo2docker/pull/1306) ([@dependabot](https://github.com/dependabot))
+- build(deps): bump docker/setup-buildx-action from 2 to 3 [#1305](https://github.com/jupyterhub/repo2docker/pull/1305) ([@dependabot](https://github.com/dependabot))
+- Update conda and mamba [#1299](https://github.com/jupyterhub/repo2docker/pull/1299) ([@SylvainCorlay](https://github.com/SylvainCorlay))
+- Point to official documentation for handling JupyterLab workspace [#1294](https://github.com/jupyterhub/repo2docker/pull/1294) ([@fcollonval](https://github.com/fcollonval))
+- Fix rstudio-build selection [#1293](https://github.com/jupyterhub/repo2docker/pull/1293) ([@yamaton](https://github.com/yamaton))
+- [pre-commit.ci] pre-commit autoupdate [#1291](https://github.com/jupyterhub/repo2docker/pull/1291) ([@pre-commit-ci](https://github.com/pre-commit-ci))
+
+### Contributors to this release
+
+([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2023-06-13&to=2024-03-28&type=c))
+
+[@annakrystalli](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aannakrystalli+updated%3A2023-06-13..2024-03-28&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2023-06-13..2024-03-28&type=Issues) | [@bollwyvl](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abollwyvl+updated%3A2023-06-13..2024-03-28&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2023-06-13..2024-03-28&type=Issues) | [@dependabot](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adependabot+updated%3A2023-06-13..2024-03-28&type=Issues) | [@dolfinus](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adolfinus+updated%3A2023-06-13..2024-03-28&type=Issues) | [@fcollonval](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afcollonval+updated%3A2023-06-13..2024-03-28&type=Issues) | [@felder](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afelder+updated%3A2023-06-13..2024-03-28&type=Issues) | [@haarli](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ahaarli+updated%3A2023-06-13..2024-03-28&type=Issues) | [@hiroyuki-sato](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ahiroyuki-sato+updated%3A2023-06-13..2024-03-28&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2023-06-13..2024-03-28&type=Issues) | [@mathieuboudreau](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amathieuboudreau+updated%3A2023-06-13..2024-03-28&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2023-06-13..2024-03-28&type=Issues) | [@pre-commit-ci](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apre-commit-ci+updated%3A2023-06-13..2024-03-28&type=Issues) | [@rgaiacs](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Argaiacs+updated%3A2023-06-13..2024-03-28&type=Issues) | [@ryanlovett](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aryanlovett+updated%3A2023-06-13..2024-03-28&type=Issues) | [@sgaist](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asgaist+updated%3A2023-06-13..2024-03-28&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2023-06-13..2024-03-28&type=Issues) | [@TimoRoth](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ATimoRoth+updated%3A2023-06-13..2024-03-28&type=Issues) | [@twtw](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atwtw+updated%3A2023-06-13..2024-03-28&type=Issues) | [@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2023-06-13..2024-03-28&type=Issues) | [@yamaton](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayamaton+updated%3A2023-06-13..2024-03-28&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2023-06-13..2024-03-28&type=Issues)
+
 ## Version 2023.06.0
 
 ([full changelog](https://github.com/jupyterhub/repo2docker/compare/2022.10.0...2023.06.0))

docs/source/config_files.rst

@@ -242,10 +242,13 @@ In the majority of cases, providing your own Dockerfile is not necessary as the
 images provide core functionality, compact image sizes, and efficient builds. We recommend
 trying the other configuration files before deciding to use your own Dockerfile.
 
-With Dockerfiles, a regular Docker build will be performed.
+Try the ``--appendix`` :ref:`CLI flag <usage-cli>` as a last resort. If you
+still can't achieve your goals, you should create a Dockerfile from scratch to
+define your image.
 
 .. note::
-    If a Dockerfile is present, all other configuration files will be ignored.
+   With Dockerfiles, a regular Docker build will be performed. All other
+   configuration files will be ignored.
 
 See the `Advanced Binder Documentation <https://mybinder.readthedocs.io/en/latest/tutorials/dockerfile.html>`_ for
 best-practices with Dockerfiles.

docs/source/faq.rst

@@ -115,6 +115,9 @@ flag for each variable that you want to define.
 
 For example ``jupyter-repo2docker -e VAR1=val1 -e VAR2=val2 ...``
 
+
+.. _faq-dockerfile-bootstrap:
+
 Can I use repo2docker to bootstrap my own Dockerfile?
 -----------------------------------------------------
 
@@ -189,3 +192,33 @@ tool called `source2image <https://github.com/openshift/source-to-image/>`_.
 This is an excellent open tool for containerization, but we
 ultimately decided that it did not fit the use-case we wanted to address. For more information,
 `here <https://github.com/yuvipanda/words/blob/fd096dd49d87e624acd8bdf6d13c0cecb930bb3f/content/post/why-not-s2i.md>`_ is a short blog post about the decision and the reasoning behind it.
+
+
+Where are my ``man`` pages?
+---------------------------
+
+The base image used by ``repo2docker`` is `Minimal Ubuntu
+<https://wiki.ubuntu.com/Minimal>`_ version 18. In Minimal Ubuntu, ``man``
+pages are disabled to reduce image size. If your use case is interactive
+computing or education, you may want to re-enable ``man`` pages. To do this,
+use the ``--appendix`` :ref:`CLI flag <usage-cli>` to pass in additional
+``Dockerfile`` instructions, for example:
+
+.. code-block:: dockerfile
+
+   # Re-enable man pages disabled in Ubuntu 18 minimal image
+   # https://wiki.ubuntu.com/Minimal
+   USER root
+   RUN yes | unminimize
+   # NOTE: $NB_PYTHON_PREFIX is the same as $CONDA_PREFIX at run-time.
+   # $CONDA_PREFIX isn't available in this context.
+   # NOTE: Prepending ensures a working path; if $MANPATH was previously empty,
+   # the trailing colon ensures that system paths are searched.
+   ENV MANPATH="${NB_PYTHON_PREFIX}/share/man:${MANPATH}"
+   RUN mandb
+
+   # Revert to default user
+   USER ${NB_USER}
+
+This appendix can be used by, for example, writing it to a file named
+``appendix`` and executing ``repo2docker --appendix "$(cat appendix)" .``.

docs/source/usage.rst

@@ -106,14 +106,21 @@ by ``repo2docker`` to see how to configure the build process.
    :ref:`configuration files <config-files>`.
 
 
+.. _usage-debugging-with-debug-and-no-build:
+
 Debugging repo2docker with ``--debug`` and ``--no-build``
 =========================================================
 
+.. warning::
+
+   This feature is *not* for bootstrapping a custom Dockerfile. Please see the
+   :ref:`relevant FAQ entry <faq-dockerfile-bootstrap>`.
+
 To debug the docker image being built, pass the ``--debug`` parameter:
 
-  .. code-block:: bash
+.. code-block:: bash
 
-     jupyter-repo2docker --debug https://github.com/norvig/pytudes
+   jupyter-repo2docker --debug https://github.com/norvig/pytudes
 
 This will print the generated ``Dockerfile``, build it, and run it.
 
@@ -122,11 +129,13 @@ pass ``--no-build`` to the commandline. This ``Dockerfile`` output
 is for **debugging purposes** of ``repo2docker`` only - it can not
 be used by docker directly.
 
-  .. code-block:: bash
+.. code-block:: bash
 
-     jupyter-repo2docker --no-build --debug https://github.com/norvig/pytudes
+   jupyter-repo2docker --no-build --debug https://github.com/norvig/pytudes
 
 
+.. _usage-cli:
+
 Command line API
 ================
 

repo2docker/buildpacks/conda/install-base-env.bash

@@ -5,8 +5,8 @@ set -ex
 
 cd $(dirname $0)
 
-export MAMBA_VERSION=1.5.1
-export CONDA_VERSION=23.7.4
+export MAMBA_VERSION=1.5.7
+export CONDA_VERSION=24.3.0
 
 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2"
 

tests/conda/py35-binder-dir/verify

@@ -16,13 +16,13 @@ v = out.split()[1]
 assert v[:3] == "3.5", out
 
 out = sh(["micromamba", "--version"])
-assert out == "1.5.1", out
+assert out == "1.5.7", out
 
 out = sh(["mamba", "--version"])
 assert (
     out
-    == """mamba 1.5.1
-conda 23.7.4"""
+    == """mamba 1.5.7
+conda 24.3.0"""
 ), out
 
 sh([kernel_python, "-c", "import numpy"])