Merge pull request #1344 from jupyterhub/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate
2024-05-07 07:39:29 +02:00 · 2024-05-06 22:03:34 +00:00 · 2024-04-02 09:54:26 +02:00 · 2024-04-01 22:10:42 +00:00 · 2024-03-31 20:43:31 +02:00 · 2024-03-28 19:13:23 +00:00
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@ -32,13 +32,13 @@ jobs:
    runs-on: ubuntu-22.04
    steps:
      - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
        with:
          fetch-depth: 0

      # https://github.com/docker/build-push-action
      - name: Build Docker image
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
        with:
          context: .
          tags: jupyter/repo2docker:pr
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@ -31,8 +31,8 @@ jobs:
  build-n-publish:
    runs-on: ubuntu-22.04
    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
        with:
          python-version: "3.9"

@ -47,7 +47,7 @@ jobs:
          ls -l dist

      # ref: https://github.com/actions/upload-artifact#readme
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
        with:
          name: repo2docker-${{ github.sha }}
          path: "dist/*"
@ -86,7 +86,7 @@ jobs:
          echo "Publishing to $REGISTRY"

      # versioneer requires the full git history for non-tags
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
        with:
          fetch-depth: 0

@ -94,10 +94,10 @@ jobs:
      # https://github.com/docker/build-push-action/tree/v2.4.0#usage
      # https://github.com/docker/build-push-action/blob/v2.4.0/docs/advanced/multi-platform.md
      - name: Set up QEMU (for docker buildx)
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3

      - name: Set up Docker Buildx (for multi-arch builds)
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
        with:
          # Allows pushing to registry on localhost:5000
          driver-opts: network=host
@ -124,7 +124,7 @@ jobs:
          echo "TAGS=$TAGS" >> $GITHUB_ENV

      - name: Build and push repo2docker
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
        with:
          context: .
          platforms: linux/amd64,linux/arm64
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@ -69,8 +69,8 @@ jobs:
            repo_type: venv

    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
        with:
          python-version: "${{ matrix.python_version }}"

@ -93,4 +93,4 @@ jobs:
        run: |
          pytest --verbose --color=yes --durations=10 --cov=repo2docker tests/${{ matrix.repo_type }}

-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@ -11,7 +11,7 @@
 repos:
  # Autoformat: Python code, syntax patterns are modernized
  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.4.0
+    rev: v3.15.2
    hooks:
      - id: pyupgrade
        args:
@ -23,7 +23,7 @@ repos:

  # Autoformat: Python code
  - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.4.2
    hooks:
      - id: black
        args:
@ -36,7 +36,7 @@ repos:

  # Autoformat: Python code
  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
    hooks:
      - id: isort
        args:
@ -44,7 +44,7 @@ repos:

  # Autoformat: markdown
  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.9-for-vscode
+    rev: v4.0.0-alpha.8
    hooks:
      - id: prettier
        files: ".md"
--- a/24
+++ b/24
@ -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
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@ -2,6 +2,6 @@ build
 conda-lock
 pre-commit
 pytest-cov
-pytest>=4.6
+pytest>=7
 pyyaml
 requests_mock
--- a/docs/source/changelog.md
+++ b/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))
--- a/docs/source/config_files.rst
+++ b/docs/source/config_files.rst
@ -233,6 +233,8 @@ To see an example repository visit
 `nix binder example <https://github.com/binder-examples/nix>`_.


+.. _dockerfile:
+
 ``Dockerfile`` - Advanced environments
 ======================================

--- a/docs/source/design.md
+++ b/docs/source/design.md
@ -49,7 +49,7 @@ Many ingredients go into making an image from a repository:

 `repo2docker` controls the first two, the user controls the third one. The current
 policy for the version of the base image is that we will use the current LTS
-version Bionic Beaver (18.04) for the foreseeable future.
+version Jammy Jellyfish (22.04) for the foreseeable future.

 The version of `repo2docker` used to build an image can influence which packages
 are installed by default and which features are supported during the build
--- a/docs/source/faq.rst
+++ b/docs/source/faq.rst
@ -62,11 +62,11 @@ Julia versions 0.6.x and earlier are supported via a :ref:`REQUIRE <REQUIRE>` fi
 R
 ~

-The default version of R is currently R 3.6.1. You can select the version of
+The default version of R is currently R 4.2. You can select the version of
 R you want to use by specifying it in the :ref:`runtime.txt <runtime.txt>`
 file.

-We support R versions 3.4, 3.5 and 3.6.
+We support R versions 3.4, 3.5, 3.6, 4.0, 4.1 and 4.2.


 Why is my repository failing to build with ``ResolvePackageNotFound`` ?
--- a/docs/source/howto/base_image.md
+++ b/docs/source/howto/base_image.md
@ -3,11 +3,11 @@
 You may change the base image used in the `Dockerfile` that creates images by repo2docker.
 This is equivalent to changing the `FROM <base_image>` in the Dockerfile.

-To do so, use the `base_image` traitlet when invoking `repo2docker`.
+To do so, use the `base_image` traitlet when invoking `repo2docker` (ex: `repo2docker --Repo2Docker.base_image=image_name`).
 Note that this is not configurable by individual repositories, it is configured when you invoke the `repo2docker` command.

 ```{note}
-By default repo2docker builds on top of the `buildpack-deps:bionic` base image, an Ubuntu-based image.
+By default repo2docker builds on top of the `buildpack-deps:jammy` base image, an Ubuntu-based image.
 ```

 ## Requirements for your base image
@ -26,8 +26,8 @@ Changing the base image may have an impact on the reproducibility of repositorie
 There are **no guarantees that repositories will behave the same way as other repo2docker builds if you change the base image**.
 For example these are two scenarios that would make your repositories non-reproducible:

- **Your base image is different from `Ubuntu:bionic`.**
-  If you change the base image in a way that is different from repo2docker's default (the Ubuntu `bionic` image), then repositories that **you** build with repo2docker may be significantly different from those that **other** instances of repo2docker build (e.g., those from [`mybinder.org`](https://mybinder.org)).
+- **Your base image is different from `Ubuntu:jammy`.**
+  If you change the base image in a way that is different from repo2docker's default (the Ubuntu `jammy` image), then repositories that **you** build with repo2docker may be significantly different from those that **other** instances of repo2docker build (e.g., those from [`mybinder.org`](https://mybinder.org)).
 - **Your base image changes over time.**
  If you choose a base image that changes its composition over time (e.g., an image provided by some other community), then it may cause repositories build with your base image to change in unpredictable ways.
  We recommend choosing a base image that you know to be stable and trustworthy.
--- a/docs/source/howto/breaking_changes.md
+++ b/docs/source/howto/breaking_changes.md
@ -0,0 +1,26 @@
+# Deal with breaking changes in repo2docker
+
+Repo2docker occasionally has to make breaking changes in how repositories are built.
+
+## Upgrade of base image from Ubuntu 18.04 to 22.04
+
+The base image used by repo2docker was [upgraded from Ubuntu 18.04 to Ubuntu 22.04](https://github.com/jupyterhub/repo2docker/pull/1287) in version 2023.10.0 due to Ubuntu 18.04 going out of support.
+
+This is unlikely to affect you unless you are using {ref}`apt.txt <apt.txt>`.
+
+{ref}`apt.txt <apt.txt>` installs packages from the official Ubuntu package repositories, and is intrinsically tied to the Ubuntu version.
+Many packages will be available in both Ubuntu 18.04 and Ubuntu 22.04, however some may be renamed (for example if multiple incompatible versions are available).
+
+Some packages may be removed, or may not be compatible with the previous version.
+In this case you should see if your packages can be installed using a {ref}`Conda environment.yml file <environment.yml>` using either the default [conda-forge channel](https://conda-forge.org/feedstock-outputs/) or in one of the many [third-party channels](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/channels.html).
+
+Alternatively you can try installing the packages from source, using a {ref}`postBuild <postBuild>` script.
+
+As a last resort you can install an older version of repo2docker locally, build your image, push it to a public container registry such as [Docker Hub](https://hub.docker.com/), [GitHub Container Registry](https://docs.github.com/en/packages/guides/about-github-container-registry) or [quay.io](https://quay.io/), and replace your repository's repo2docker configuration with a minimal {ref}`Dockerfile <dockerfile>` containing just:
+
+```dockerfile
+FROM <registry>/<username>/<image>:<tag>
+```
+
+This image will contain a frozen version of your repository at the time the image was built.
+You will need to rebuild and push it everytime your repository is modified.
--- a/docs/source/howto/index.rst
+++ b/docs/source/howto/index.rst
@ -13,6 +13,7 @@ Select from the pages listed below to get started.
   languages
   export_environment
   lab_workspaces
+   breaking_changes
   jupyterhub_images
   deploy
   base_image
--- a/docs/source/howto/lab_workspaces.rst
+++ b/docs/source/howto/lab_workspaces.rst
@ -14,6 +14,6 @@ another JupyterLab installation in order to share a workspace with
 someone else.

 In order to package your workspace with a repository, we recommend
-following the steps in this example repository:
+following the steps in the documentation:

-https://github.com/ian-r-rose/binder-workspace-demo/
+https://jupyterlab.readthedocs.io/en/stable/user/binder.html#customize-the-layout
--- a/repo2docker/init.py
+++ b/repo2docker/init.py
@ -3,4 +3,7 @@ from ._version import get_versions
 __version__ = get_versions()["version"]
 del get_versions

+from . import _version
 from .app import Repo2Docker
+
+__version__ = _version.get_versions()["version"]
--- a/repo2docker/_version.py
+++ b/repo2docker/_version.py
@ -4,19 +4,22 @@
 # directories (produced by setup.py build) will contain a much shorter file
 # that just contains the computed version number.

-# This file is released into the public domain. Generated by
-# versioneer-0.18 (https://github.com/warner/python-versioneer)
+# This file is released into the public domain.
+# Generated by versioneer-0.29
+# https://github.com/python-versioneer/python-versioneer

 """Git implementation of _version.py."""

 import errno
+import functools
 import os
 import re
 import subprocess
 import sys
+from typing import Any, Callable, Dict, List, Optional, Tuple


-def get_keywords():
+def get_keywords() -> Dict[str, str]:
    """Get the keywords needed to look up the version information."""
    # these strings will be replaced by git during git-archive.
    # setup.py/versioneer.py will grep for the variable names, so they must
@ -32,8 +35,15 @@ def get_keywords():
 class VersioneerConfig:
    """Container for Versioneer configuration parameters."""

+    VCS: str
+    style: str
+    tag_prefix: str
+    parentdir_prefix: str
+    versionfile_source: str
+    verbose: bool

-def get_config():
+
+def get_config() -> VersioneerConfig:
    """Create, populate and return the VersioneerConfig() object."""
    # these strings are filled in when 'setup.py versioneer' creates
    # _version.py
@ -51,14 +61,14 @@ class NotThisMethod(Exception):
    """Exception raised if a method is not valid for the current scenario."""


-LONG_VERSION_PY = {}
-HANDLERS = {}
+LONG_VERSION_PY: Dict[str, str] = {}
+HANDLERS: Dict[str, Dict[str, Callable]] = {}


-def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
+def register_vcs_handler(vcs: str, method: str) -> Callable:  # decorator
+    """Create decorator to mark a method as the handler of a VCS."""

-    def decorate(f):
+    def decorate(f: Callable) -> Callable:
        """Store f in HANDLERS[vcs][method]."""
        if vcs not in HANDLERS:
            HANDLERS[vcs] = {}
@ -68,24 +78,39 @@ def register_vcs_handler(vcs, method):  # decorator
    return decorate


-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
+def run_command(
+    commands: List[str],
+    args: List[str],
+    cwd: Optional[str] = None,
+    verbose: bool = False,
+    hide_stderr: bool = False,
+    env: Optional[Dict[str, str]] = None,
+) -> Tuple[Optional[str], Optional[int]]:
    """Call the given command(s)."""
    assert isinstance(commands, list)
-    p = None
-    for c in commands:
+    process = None
+
+    popen_kwargs: Dict[str, Any] = {}
+    if sys.platform == "win32":
+        # This hides the console window if pythonw.exe is used
+        startupinfo = subprocess.STARTUPINFO()
+        startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
+        popen_kwargs["startupinfo"] = startupinfo
+
+    for command in commands:
        try:
-            dispcmd = str([c] + args)
+            dispcmd = str([command] + args)
            # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen(
-                [c] + args,
+            process = subprocess.Popen(
+                [command] + args,
                cwd=cwd,
                env=env,
                stdout=subprocess.PIPE,
                stderr=(subprocess.PIPE if hide_stderr else None),
+                **popen_kwargs,
            )
            break
-        except OSError:
-            e = sys.exc_info()[1]
+        except OSError as e:
            if e.errno == errno.ENOENT:
                continue
            if verbose:
@ -96,18 +121,20 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
        if verbose:
            print(f"unable to find command, tried {commands}")
        return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
-    if p.returncode != 0:
+    stdout = process.communicate()[0].strip().decode()
+    if process.returncode != 0:
        if verbose:
            print("unable to run %s (error)" % dispcmd)
            print("stdout was %s" % stdout)
-        return None, p.returncode
-    return stdout, p.returncode
+        return None, process.returncode
+    return stdout, process.returncode


-def versions_from_parentdir(parentdir_prefix, root, verbose):
+def versions_from_parentdir(
+    parentdir_prefix: str,
+    root: str,
+    verbose: bool,
+) -> Dict[str, Any]:
    """Try to determine the version from the parent directory name.

    Source tarballs conventionally unpack into a directory that includes both
@ -116,7 +143,7 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
    """
    rootdirs = []

-    for i in range(3):
+    for _ in range(3):
        dirname = os.path.basename(root)
        if dirname.startswith(parentdir_prefix):
            return {
@ -126,9 +153,8 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
                "error": None,
                "date": None,
            }
-        else:
-            rootdirs.append(root)
-            root = os.path.dirname(root)  # up a level
+        rootdirs.append(root)
+        root = os.path.dirname(root)  # up a level

    if verbose:
        print(
@ -139,41 +165,48 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):


@register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs):
+def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
    """Extract version information from the given file."""
    # the code embedded in _version.py can just fetch the value of these
    # keywords. When used from setup.py, we don't want to import _version.py,
    # so we do it with a regexp instead. This function is not used from
    # _version.py.
-    keywords = {}
+    keywords: Dict[str, str] = {}
    try:
-        f = open(versionfile_abs)
-        for line in f.readlines():
-            if line.strip().startswith("git_refnames ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["refnames"] = mo.group(1)
-            if line.strip().startswith("git_full ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["full"] = mo.group(1)
-            if line.strip().startswith("git_date ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["date"] = mo.group(1)
-        f.close()
+        with open(versionfile_abs) as fobj:
+            for line in fobj:
+                if line.strip().startswith("git_refnames ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["refnames"] = mo.group(1)
+                if line.strip().startswith("git_full ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["full"] = mo.group(1)
+                if line.strip().startswith("git_date ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["date"] = mo.group(1)
    except OSError:
        pass
    return keywords


@register_vcs_handler("git", "keywords")
-def git_versions_from_keywords(keywords, tag_prefix, verbose):
+def git_versions_from_keywords(
+    keywords: Dict[str, str],
+    tag_prefix: str,
+    verbose: bool,
+) -> Dict[str, Any]:
    """Get version information from git keywords."""
-    if not keywords:
-        raise NotThisMethod("no keywords at all, weird")
+    if "refnames" not in keywords:
+        raise NotThisMethod("Short version file found")
    date = keywords.get("date")
    if date is not None:
+        # Use only the last line.  Previous lines may contain GPG signature
+        # information.
+        date = date.splitlines()[-1]
+
        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
        # -like" string, which we must then edit to make compliant), because
@ -208,6 +241,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
        # sorting will prefer e.g. "2.0" over "2.0rc1"
        if ref.startswith(tag_prefix):
            r = ref[len(tag_prefix) :]
+            # Filter out refs that exactly match prefix or that don't start
+            # with a number once the prefix is stripped (mostly a concern
+            # when prefix is '')
+            if not re.match(r"\d", r):
+                continue
            if verbose:
                print("picking %s" % r)
            return {
@ -230,7 +268,9 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):


@register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+def git_pieces_from_vcs(
+    tag_prefix: str, root: str, verbose: bool, runner: Callable = run_command
+) -> Dict[str, Any]:
    """Get version from 'git describe' in the root of the source tree.

    This only gets called if the git-archive 'subst' keywords were *not*
@ -241,7 +281,14 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
    if sys.platform == "win32":
        GITS = ["git.cmd", "git.exe"]

-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
+    # GIT_DIR can interfere with correct operation of Versioneer.
+    # It may be intended to be passed to the Versioneer-versioned project,
+    # but that should not change where we get our version from.
+    env = os.environ.copy()
+    env.pop("GIT_DIR", None)
+    runner = functools.partial(runner, env=env)
+
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=not verbose)
    if rc != 0:
        if verbose:
            print("Directory %s not under git control" % root)
@ -249,7 +296,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):

    # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
    # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(
+    describe_out, rc = runner(
        GITS,
        [
            "describe",
@ -258,7 +305,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
            "--always",
            "--long",
            "--match",
-            "%s*" % tag_prefix,
+            f"{tag_prefix}[[:digit:]]*",
        ],
        cwd=root,
    )
@ -266,16 +313,48 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
    if describe_out is None:
        raise NotThisMethod("'git describe' failed")
    describe_out = describe_out.strip()
-    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root)
    if full_out is None:
        raise NotThisMethod("'git rev-parse' failed")
    full_out = full_out.strip()

-    pieces = {}
+    pieces: Dict[str, Any] = {}
    pieces["long"] = full_out
    pieces["short"] = full_out[:7]  # maybe improved later
    pieces["error"] = None

+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root)
+    # --abbrev-ref was added in git-1.6.3
+    if rc != 0 or branch_name is None:
+        raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
+    branch_name = branch_name.strip()
+
+    if branch_name == "HEAD":
+        # If we aren't exactly on a branch, pick a branch which represents
+        # the current commit. If all else fails, we are on a branchless
+        # commit.
+        branches, rc = runner(GITS, ["branch", "--contains"], cwd=root)
+        # --contains was added in git-1.5.4
+        if rc != 0 or branches is None:
+            raise NotThisMethod("'git branch --contains' returned error")
+        branches = branches.split("\n")
+
+        # Remove the first line if we're running detached
+        if "(" in branches[0]:
+            branches.pop(0)
+
+        # Strip off the leading "* " from the list of branches.
+        branches = [branch[2:] for branch in branches]
+        if "master" in branches:
+            branch_name = "master"
+        elif not branches:
+            branch_name = None
+        else:
+            # Pick the first branch that is returned. Good or bad.
+            branch_name = branches[0]
+
+    pieces["branch"] = branch_name
+
    # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
    # TAG might have hyphens.
    git_describe = describe_out
@ -292,8 +371,8 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
        # TAG-NUM-gHEX
        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
        if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = f"unable to parse git-describe output: '{describe_out}'"
+            # unparsable. Maybe git-describe is misbehaving?
+            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
            return pieces

        # tag
@ -302,9 +381,10 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
            if verbose:
                fmt = "tag '%s' doesn't start with prefix '%s'"
                print(fmt % (full_tag, tag_prefix))
-            pieces[
-                "error"
-            ] = f"tag '{full_tag}' doesn't start with prefix '{tag_prefix}'"
+            pieces["error"] = "tag '{}' doesn't start with prefix '{}'".format(
+                full_tag,
+                tag_prefix,
+            )
            return pieces
        pieces["closest-tag"] = full_tag[len(tag_prefix) :]

@ -317,26 +397,27 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
    else:
        # HEX: no tags
        pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
-        pieces["distance"] = int(count_out)  # total number of commits
+        out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root)
+        pieces["distance"] = len(out.split())  # total number of commits

    # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[
-        0
-    ].strip()
+    date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
+    # Use only the last line.  Previous lines may contain GPG signature
+    # information.
+    date = date.splitlines()[-1]
    pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)

    return pieces


-def plus_or_dot(pieces):
+def plus_or_dot(pieces: Dict[str, Any]) -> str:
    """Return a + if we don't already have one, else return a ."""
    if "+" in pieces.get("closest-tag", ""):
        return "."
    return "+"


-def render_pep440(pieces):
+def render_pep440(pieces: Dict[str, Any]) -> str:
    """Build up version string, with post-release "local version identifier".

    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
@ -360,23 +441,70 @@ def render_pep440(pieces):
    return rendered


-def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
+def render_pep440_branch(pieces: Dict[str, Any]) -> str:
+    """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] .
+
+    The ".dev0" means not master branch. Note that .dev0 sorts backwards
+    (a feature branch will appear "older" than the master branch).

    Exceptions:
-    1: no tags. 0.post.devDISTANCE
+    1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty]
    """
    if pieces["closest-tag"]:
        rendered = pieces["closest-tag"]
-        if pieces["distance"]:
-            rendered += ".post.dev%d" % pieces["distance"]
+        if pieces["distance"] or pieces["dirty"]:
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
    else:
        # exception #1
-        rendered = "0.post.dev%d" % pieces["distance"]
+        rendered = "0"
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
    return rendered


-def render_pep440_post(pieces):
+def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]:
+    """Split pep440 version string at the post-release segment.
+
+    Returns the release segments before the post-release and the
+    post-release version number (or -1 if no post-release segment is present).
+    """
+    vc = str.split(ver, ".post")
+    return vc[0], int(vc[1] or 0) if len(vc) == 2 else None
+
+
+def render_pep440_pre(pieces: Dict[str, Any]) -> str:
+    """TAG[.postN.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post0.devDISTANCE
+    """
+    if pieces["closest-tag"]:
+        if pieces["distance"]:
+            # update the post release segment
+            tag_version, post_version = pep440_split_post(pieces["closest-tag"])
+            rendered = tag_version
+            if post_version is not None:
+                rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"])
+            else:
+                rendered += ".post0.dev%d" % (pieces["distance"])
+        else:
+            # no commits, use the tag as the version
+            rendered = pieces["closest-tag"]
+    else:
+        # exception #1
+        rendered = "0.post0.dev%d" % pieces["distance"]
+    return rendered
+
+
+def render_pep440_post(pieces: Dict[str, Any]) -> str:
    """TAG[.postDISTANCE[.dev0]+gHEX] .

    The ".dev0" means dirty. Note that .dev0 sorts backwards
@ -403,12 +531,41 @@ def render_pep440_post(pieces):
    return rendered


-def render_pep440_old(pieces):
+def render_pep440_post_branch(pieces: Dict[str, Any]) -> str:
+    """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] .
+
+    The ".dev0" means not master branch.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_old(pieces: Dict[str, Any]) -> str:
    """TAG[.postDISTANCE[.dev0]] .

    The ".dev0" means dirty.

-    Eexceptions:
+    Exceptions:
    1: no tags. 0.postDISTANCE[.dev0]
    """
    if pieces["closest-tag"]:
@ -425,7 +582,7 @@ def render_pep440_old(pieces):
    return rendered


-def render_git_describe(pieces):
+def render_git_describe(pieces: Dict[str, Any]) -> str:
    """TAG[-DISTANCE-gHEX][-dirty].

    Like 'git describe --tags --dirty --always'.
@ -445,7 +602,7 @@ def render_git_describe(pieces):
    return rendered


-def render_git_describe_long(pieces):
+def render_git_describe_long(pieces: Dict[str, Any]) -> str:
    """TAG-DISTANCE-gHEX[-dirty].

    Like 'git describe --tags --dirty --always -long'.
@ -465,7 +622,7 @@ def render_git_describe_long(pieces):
    return rendered


-def render(pieces, style):
+def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]:
    """Render the given version pieces into the requested style."""
    if pieces["error"]:
        return {
@ -481,10 +638,14 @@ def render(pieces, style):

    if style == "pep440":
        rendered = render_pep440(pieces)
+    elif style == "pep440-branch":
+        rendered = render_pep440_branch(pieces)
    elif style == "pep440-pre":
        rendered = render_pep440_pre(pieces)
    elif style == "pep440-post":
        rendered = render_pep440_post(pieces)
+    elif style == "pep440-post-branch":
+        rendered = render_pep440_post_branch(pieces)
    elif style == "pep440-old":
        rendered = render_pep440_old(pieces)
    elif style == "git-describe":
@ -503,7 +664,7 @@ def render(pieces, style):
    }


-def get_versions():
+def get_versions() -> Dict[str, Any]:
    """Get version information or return default if unable to do so."""
    # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
    # __file__, we can work backwards from there to the root. Some
@ -523,7 +684,7 @@ def get_versions():
        # versionfile_source is the relative path from the top of the source
        # tree (where the .git directory might live) to this file. Invert
        # this to find the root from __file__.
-        for i in cfg.versionfile_source.split("/"):
+        for _ in cfg.versionfile_source.split("/"):
            root = os.path.dirname(root)
    except NameError:
        return {
--- a/repo2docker/app.py
+++ b/repo2docker/app.py
@ -7,6 +7,7 @@ Usage:

    python -m repo2docker https://github.com/you/your-repo
 """
+
 import getpass
 import json
 import logging
@ -448,7 +449,7 @@ class Repo2Docker(Application):
    )

    base_image = Unicode(
-        "docker.io/library/buildpack-deps:bionic",
+        "docker.io/library/buildpack-deps:jammy",
        config=True,
        help="""
        Base image to use when building docker images.
--- a/repo2docker/buildpacks/_r_base.py
+++ b/repo2docker/buildpacks/_r_base.py
@ -3,6 +3,7 @@ Base information for using R in BuildPacks.

 Keeping this in r.py would lead to cyclic imports.
 """
+
 from ..semver import parse_version as V


@ -28,7 +29,7 @@ def rstudio_base_scripts(r_version):
    rstudio_openssl1_sha256sum = (
        "bb88e37328c304881e60d6205d7dac145525a5c2aaaf9da26f1cb625b7d47e6e"
    )
-    rsession_proxy_version = "2.0.1"
+    rsession_proxy_version = "2.2.0"

    return [
        (
@ -38,7 +39,7 @@ def rstudio_base_scripts(r_version):
            # which will upgrade the installed version of R, undoing our pinned version
            rf"""
            apt-get update > /dev/null && \
-            if apt-cache search libssl3 > /dev/null; then \
+            if apt-cache search libssl3 | grep -q libssl3; then \
              RSTUDIO_URL="{rstudio_openssl3_url}" ;\
              RSTUDIO_HASH="{rstudio_openssl3_sha256sum}" ;\
            else \
--- a/repo2docker/buildpacks/base.py
+++ b/repo2docker/buildpacks/base.py
@ -11,6 +11,7 @@ from functools import lru_cache

 import escapism
 import jinja2
+from docker.utils.build import exclude_paths

 # Only use syntax features supported by Docker 17.09
 TEMPLATE = r"""
@ -590,16 +591,16 @@ class BuildPack:

        tar.addfile(dockerfile_tarinfo, io.BytesIO(dockerfile))

-        def _filter_tar(tar):
+        def _filter_tar(tarinfo):
            # We need to unset these for build_script_files we copy into tar
            # Otherwise they seem to vary each time, preventing effective use
            # of the cache!
            # https://github.com/docker/docker-py/pull/1582 is related
-            tar.uname = ""
-            tar.gname = ""
-            tar.uid = int(build_args.get("NB_UID", DEFAULT_NB_UID))
-            tar.gid = int(build_args.get("NB_UID", DEFAULT_NB_UID))
-            return tar
+            tarinfo.uname = ""
+            tarinfo.gname = ""
+            tarinfo.uid = int(build_args.get("NB_UID", DEFAULT_NB_UID))
+            tarinfo.gid = int(build_args.get("NB_UID", DEFAULT_NB_UID))
+            return tarinfo

        for src in sorted(self.get_build_script_files()):
            dest_path, src_path = self.generate_build_context_filename(src)
@ -608,7 +609,34 @@ class BuildPack:
        for fname in ("repo2docker-entrypoint", "python3-login"):
            tar.add(os.path.join(HERE, fname), fname, filter=_filter_tar)

-        tar.add(".", "src/", filter=_filter_tar)
+        exclude = []
+
+        for ignore_file_name in [".dockerignore", ".containerignore"]:
+            ignore_file_name = self.binder_path(ignore_file_name)
+            if os.path.exists(ignore_file_name):
+                with open(ignore_file_name) as ignore_file:
+                    cleaned_lines = [
+                        line.strip() for line in ignore_file.read().splitlines()
+                    ]
+                    exclude.extend(
+                        [
+                            line
+                            for line in cleaned_lines
+                            if line != "" and line[0] != "#"
+                        ]
+                    )
+
+        files_to_add = exclude_paths(".", exclude)
+
+        if files_to_add:
+            for item in files_to_add:
+                tar.add(item, f"src/{item}", filter=_filter_tar)
+        else:
+            # Either the source was empty or everything was filtered out.
+            # In any case, create an src dir so the build can proceed.
+            src = tarfile.TarInfo("src")
+            src.type = tarfile.DIRTYPE
+            tar.addfile(src)

        tar.close()
        tarf.seek(0)
--- a/repo2docker/buildpacks/conda/init.py
+++ b/repo2docker/buildpacks/conda/init.py
@ -1,4 +1,5 @@
 """BuildPack for conda environments"""
+
 import os
 import re
 import warnings
@ -193,15 +194,15 @@ class CondaBuildPack(BaseImage):
                raise ValueError(
                    f"Python version {py_version} on {conda_platform} is not supported!"
                )
-            files[
-                f"conda/{lockfile_name}"
-            ] = self._kernel_environment_file = "/tmp/env/kernel-environment.lock"
+            files[f"conda/{lockfile_name}"] = self._kernel_environment_file = (
+                "/tmp/env/kernel-environment.lock"
+            )

            requirements_file_name = f"requirements.py-{py_version}.pip"
            if os.path.exists(os.path.join(HERE, requirements_file_name)):
-                files[
-                    f"conda/{requirements_file_name}"
-                ] = self._kernel_requirements_file = "/tmp/env/kernel-requirements.txt"
+                files[f"conda/{requirements_file_name}"] = (
+                    self._kernel_requirements_file
+                ) = "/tmp/env/kernel-requirements.txt"
        else:
            # server and kernel are the same
            server_py_version = py_version
@ -216,15 +217,15 @@ class CondaBuildPack(BaseImage):
                f"Python version {server_py_version} on {conda_platform} is not supported!"
            )

-        files[
-            "conda/" + conda_frozen_name
-        ] = self._nb_environment_file = "/tmp/env/environment.lock"
+        files["conda/" + conda_frozen_name] = self._nb_environment_file = (
+            "/tmp/env/environment.lock"
+        )

        # add requirements.txt, if present
        if os.path.exists(os.path.join(HERE, pip_frozen_name)):
-            files[
-                "conda/" + pip_frozen_name
-            ] = self._nb_requirements_file = "/tmp/env/requirements.txt"
+            files["conda/" + pip_frozen_name] = self._nb_requirements_file = (
+                "/tmp/env/requirements.txt"
+            )

        files.update(super().get_build_script_files())
        return files
--- a/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock
@ -1,167 +1,175 @@
 # AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-06-08 09:35:19 UTC
+# Frozen on 2023-10-14 22:06:18 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 5e20d8617672faf1f048550dc6ffdcf6288c12f1faf23a9051314056a752d9f3
+# input_hash: d4de4d52232becb85e22651d47e3ee37eda3e6773f0cda97e029623595714734
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@ -1,166 +1,173 @@
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--- a/repo2docker/buildpacks/conda/environment.py-3.10.yml
+++ b/repo2docker/buildpacks/conda/environment.py-3.10.yml
@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-06-08 09:35:19 UTC
+# Generated on 2023-10-14 22:06:18 UTC
 channels:
 - conda-forge
 dependencies:
--- a/repo2docker/buildpacks/conda/environment.py-3.11-linux-64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.11-linux-64.lock
@ -1,168 +1,176 @@
 # AUTO GENERATED FROM environment.py-3.11.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-06-08 09:35:47 UTC
+# Frozen on 2023-10-14 22:06:48 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 3896c7e12b9461937f193ac022a4426948268f5b348da74e57eeacea703149a4
+# input_hash: d7858459013cde39e2cf3380f5eefa3195c013a2a891b6cce2de3c687db9c116
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--- a/repo2docker/buildpacks/conda/environment.py-3.11-linux-aarch64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.11-linux-aarch64.lock
@ -1,167 +1,174 @@
 # AUTO GENERATED FROM environment.py-3.11.yml, DO NOT MANUALLY MODIFY
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--- a/repo2docker/buildpacks/conda/environment.py-3.11.yml
+++ b/repo2docker/buildpacks/conda/environment.py-3.11.yml
@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-06-08 09:35:47 UTC
+# Generated on 2023-10-14 22:06:48 UTC
 channels:
 - conda-forge
 dependencies:
--- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock
@ -1,158 +1,164 @@
 # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-06-08 09:33:53 UTC
+# Frozen on 2023-10-14 22:04:48 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 2339ad954e3f369212967cce974e168db8116914593597b2d8fe8742b677dd60
+# input_hash: 5915c99fbcf718ecb070006efbc921e7cbe0a9732a6187bb88b2c177f7e82f8d
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--- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock
@ -1,114 +1,110 @@
 # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
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--- a/repo2docker/buildpacks/conda/environment.py-3.7.yml
+++ b/repo2docker/buildpacks/conda/environment.py-3.7.yml
@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-06-08 09:33:53 UTC
+# Generated on 2023-10-14 22:04:48 UTC
 channels:
 - conda-forge
 dependencies:
--- a/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock
@ -1,166 +1,174 @@
 # AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-06-08 09:34:21 UTC
+# Frozen on 2023-10-14 22:05:18 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 36ddbee99d9fd787926a944b240a11b032e89e3c46dc4666bc9f0a4cff2f385c
+# input_hash: 06bcc16f99337eabba948f7b565f8f19943cd96f5d3c068090a296c29c047ba9
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--- a/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock
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@ -1,165 +1,172 @@
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--- a/repo2docker/buildpacks/conda/environment.py-3.8.yml
+++ b/repo2docker/buildpacks/conda/environment.py-3.8.yml
@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-06-08 09:34:21 UTC
+# Generated on 2023-10-14 22:05:18 UTC
 channels:
 - conda-forge
 dependencies:
--- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock
@ -1,167 +1,175 @@
 # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-06-08 09:34:51 UTC
+# Frozen on 2023-10-14 22:05:49 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: a8b01e6cf54b5f11b1fb28a14c88acae0339819976b3ee55dd4504f09b37ab3c
+# input_hash: 99f0205247d52a0abd0dc705f3ce959255560aebd34ea60d0cc67e297e2ee7c1
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--- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock
@ -1,166 +1,173 @@
 # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-06-08 09:35:00 UTC
+# Frozen on 2023-10-14 22:05:59 UTC
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+https://conda.anaconda.org/conda-forge/linux-aarch64/sqlalchemy-2.0.22-py39h7cc1d5f_0.conda#1c74b3c81fb26ac7c50281ebe4d80d78
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-https://conda.anaconda.org/conda-forge/noarch/alembic-1.11.1-pyhd8ed1ab_0.conda#6a55e123397b42b79c48b31d1b7a91b8
-https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-21.3.0-pyhd8ed1ab_0.tar.bz2#a0b402db58f73aaab8ee0ca1025a362e
-https://conda.anaconda.org/conda-forge/linux-aarch64/jupyter_core-5.3.0-py39h4420490_0.conda#67b269d3b66a048986a891ba98959cec
-https://conda.anaconda.org/conda-forge/noarch/jupyter_events-0.6.3-pyhd8ed1ab_0.conda#d98c5196ab6ffeb0c2feca2912801353
-https://conda.anaconda.org/conda-forge/noarch/jupyter_telemetry-0.1.0-pyhd8ed1ab_1.tar.bz2#bb9ebdb6d5aa2622484aff1faceee181
+https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.8-pyhd8ed1ab_0.conda#367386d2575a0e62412448eda1012efd
+https://conda.anaconda.org/conda-forge/noarch/alembic-1.12.0-pyhd8ed1ab_0.conda#ba29026b587195548ef82444518061f7
+https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-23.1.0-pyhd8ed1ab_0.conda#3afef1f55a1366b4d3b6a0d92e2235e4
+https://conda.anaconda.org/conda-forge/noarch/isoduration-20.11.0-pyhd8ed1ab_0.tar.bz2#4cb68948e0b8429534380243d063a27a
+https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.19.1-pyhd8ed1ab_0.conda#78aff5d2af74e6537c1ca73017f01f4f
+https://conda.anaconda.org/conda-forge/linux-aarch64/jupyter_core-5.4.0-py39h4420490_0.conda#5b140264aa2a194473cb7ea5aef9f7aa
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-https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.38-pyha770c72_0.conda#59ba1bf8ea558751a0d391249a248765
+https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.39-pyha770c72_0.conda#a4986c6bb5b0d05a38855b0880a5f425
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-https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.2.0-pyhd8ed1ab_0.conda#58ca2d50c3b27b86fd7df62eaadbf9a9
-https://conda.anaconda.org/conda-forge/noarch/nbformat-5.9.0-pyhd8ed1ab_0.conda#f525a01528c3eba1d381a232a6971c6a
-https://conda.anaconda.org/conda-forge/noarch/prompt_toolkit-3.0.38-hd8ed1ab_0.conda#45b74f64d8808eda7e6f6e6b1d641fd2
-https://conda.anaconda.org/conda-forge/noarch/ipython-8.14.0-pyh41d4057_0.conda#0a0b0d8177c4a209017b356439292db8
+https://conda.anaconda.org/conda-forge/noarch/jsonschema-with-format-nongpl-4.19.1-pyhd8ed1ab_0.conda#daca0665e6fe8a376e48b9f0b5865326
+https://conda.anaconda.org/conda-forge/noarch/jupyter_client-7.4.9-pyhd8ed1ab_0.conda#5cbf9a31a19d4ef9103adb7d71fd45fd
+https://conda.anaconda.org/conda-forge/noarch/jupyter_telemetry-0.1.0-pyhd8ed1ab_1.tar.bz2#bb9ebdb6d5aa2622484aff1faceee181
+https://conda.anaconda.org/conda-forge/noarch/nbformat-5.9.2-pyhd8ed1ab_0.conda#61ba076de6530d9301a0053b02f093d2
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 https://conda.anaconda.org/conda-forge/noarch/jupyterhub-base-3.1.1-pyh2a2186d_0.conda#78fc5dfd4577a7ba172fa65eb64b6afb
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-https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.23.1-pyh210e3f2_0.conda#4b57b688e22d094d1479a35543c18e93
-https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.4.0-pyhd8ed1ab_0.conda#4456e6030a8309bdad57569b0170b6a3
-https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.0.6-pyhd8ed1ab_0.conda#68627a08556e4a273e4c7bfc84251457
-https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.6-pyhd8ed1ab_0.conda#5016f7c6845a6efd270fcee63af9a2a0
-https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.4.0-pyhd8ed1ab_0.conda#127c702e1b1eff595be82bc6a78cfce0
+https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.25.2-pyh2140261_0.conda#226f2032ec491cc6e9ce66072660e4f6
+https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.1.1-pyhd8ed1ab_0.conda#2605fae5ee27100e5f10037baebf4d41
+https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.9.2-pyhd8ed1ab_0.conda#01e4314c780ca73759c694ce3ece281f
+https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.24.0-pyhd8ed1ab_0.conda#7f0d2ec2d4954188ff23503f39823409
+https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.9.2-pyhd8ed1ab_0.conda#1ad46253f2eb46fb8c9b2c22b7ca012f
 https://conda.anaconda.org/conda-forge/noarch/jupyter-resource-usage-0.7.1-pyhd8ed1ab_0.conda#62ed54dc748d19d0cf056a3f90cc8f12
 https://conda.anaconda.org/conda-forge/noarch/jupyter_server_fileid-0.9.0-pyhd8ed1ab_0.conda#a12525b037a703d7f4512da737d700e6
-https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.22.1-pyhd8ed1ab_0.conda#fc7172a6742a7c3c4331ddd7ed463ffc
-https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.4.0-pyhd8ed1ab_0.conda#a86727968b41c20dd3d73b91632e77dc
+https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.25.0-pyhd8ed1ab_0.conda#a52834fa7e3d12abc5efdf06b2097a05
+https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.9.2-pyhd8ed1ab_0.conda#16ccaddfcfa0a1a606a9ecf6a52d6c11
 https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.3-pyhd8ed1ab_0.conda#67e0fe74c156267d9159e9133df7fd37
 https://conda.anaconda.org/conda-forge/noarch/jupyter_server_ydoc-0.8.0-pyhd8ed1ab_0.conda#780280d42fbcb2eaf654a6ba7a3e5bb5
 https://conda.anaconda.org/conda-forge/noarch/nbclassic-1.0.0-pyhb4ecaf3_1.conda#a0be31e9bd84d6eae87cdbf74c56b90b
-https://conda.anaconda.org/conda-forge/noarch/notebook-6.5.4-pyha770c72_0.conda#ec4ce3ce0a55ce21b6f5b86049b97af9
+https://conda.anaconda.org/conda-forge/noarch/notebook-6.5.6-pyha770c72_0.conda#2e2422cf19f555ef3ddbbeaf2eac7545
 https://conda.anaconda.org/conda-forge/noarch/jupyter-offlinenotebook-0.2.2-pyh1d7be83_0.tar.bz2#fe55056ce4bc4bd4953ba440270735fb
-https://conda.anaconda.org/conda-forge/noarch/jupyterlab-3.6.4-pyhd8ed1ab_0.conda#e66d4a6e36fcc92fe266932bf85fd35a
+https://conda.anaconda.org/conda-forge/noarch/jupyterlab-3.6.6-pyhd8ed1ab_0.conda#05def61d4c64b0f3161eaeb3b00cc790
 https://conda.anaconda.org/conda-forge/noarch/jupyterhub-singleuser-3.1.1-pyh2a2186d_0.conda#6d0a3394efe9ff7c0ad1ed03a6ca3720
--- a/repo2docker/buildpacks/conda/environment.py-3.9.yml
+++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml
@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-06-08 09:34:51 UTC
+# Generated on 2023-10-14 22:05:49 UTC
 channels:
 - conda-forge
 dependencies:
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@ -5,8 +5,8 @@ set -ex

 cd $(dirname $0)

-export MAMBA_VERSION=1.4.0
-export CONDA_VERSION=23.1.0
+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"

--- a/repo2docker/buildpacks/docker.py
+++ b/repo2docker/buildpacks/docker.py
@ -1,5 +1,6 @@
 """Generates a variety of Dockerfiles based on an input matrix
 """
+
 import os

 import docker
--- a/repo2docker/buildpacks/julia/julia_project.py
+++ b/repo2docker/buildpacks/julia/julia_project.py
@ -1,4 +1,5 @@
 """Generates a Dockerfile based on an input matrix for Julia"""
+
 import functools
 import os
 from functools import lru_cache
--- a/repo2docker/buildpacks/julia/julia_require.py
+++ b/repo2docker/buildpacks/julia/julia_require.py
@ -175,7 +175,7 @@ class JuliaRequireBuildPack(PythonBuildPack):
                r"""
            julia /tmp/install-repo-dependencies.jl "%(require)s"
            """
-                % {"require": require}
+                % {"require": require},
                # TODO: For some reason, `rm`ing the file fails with permission denied.
                # && rm /tmp/install-repo-dependencies.jl
            )
--- a/repo2docker/buildpacks/legacy/init.py
+++ b/repo2docker/buildpacks/legacy/init.py
@ -7,6 +7,7 @@ and IPython kernel.

 Note: This buildpack has been deprecated.
 """
+
 import logging


--- a/repo2docker/buildpacks/nix/init.py
+++ b/repo2docker/buildpacks/nix/init.py
@ -1,4 +1,5 @@
 """BuildPack for nixpkgs environments"""
+
 import os
 from functools import lru_cache

--- a/repo2docker/buildpacks/pipfile/init.py
+++ b/repo2docker/buildpacks/pipfile/init.py
@ -173,9 +173,11 @@ class PipfileBuildPack(CondaBuildPack):
                        pipenv --clear \\
                )""".format(
                    working_directory=working_directory,
-                    install_option="--ignore-pipfile"
-                    if os.path.exists(pipfile_lock)
-                    else "--skip-lock",
+                    install_option=(
+                        "--ignore-pipfile"
+                        if os.path.exists(pipfile_lock)
+                        else "--skip-lock"
+                    ),
                ),
            )
        )
--- a/repo2docker/buildpacks/python/init.py
+++ b/repo2docker/buildpacks/python/init.py
@ -1,4 +1,5 @@
 """Generates Dockerfiles based on an input matrix based on Python."""
+
 import os
 from functools import lru_cache

--- a/repo2docker/buildpacks/r.py
+++ b/repo2docker/buildpacks/r.py
@ -217,7 +217,7 @@ class RBuildPack(PythonBuildPack):
                    ),
                },
            ).json()
-            # Construct a snapshot URL that will give us binary packages for Ubuntu Bionic (18.04)
+            # Construct a snapshot URL that will give us binary packages for appropriate ubuntu version
            if "upsi" in snapshots:
                return (
                    # Env variables here are expanded by envsubst in the Dockerfile, after sourcing
@ -339,6 +339,15 @@ class RBuildPack(PythonBuildPack):
                echo "r-cran-repos=${{EXPANDED_CRAN_MIRROR_URL}}" > /etc/rstudio/rsession.conf
                """,
            ),
+            (
+                "root",
+                # Configure log-level and send to stderr
+                # Set log-level=debug to investigate problems
+                # https://docs.posit.co/ide/server-pro/server_management/logging.html
+                rf"""
+                printf '[*]\nlog-level=info\nlogger-type=stderr\n' > /etc/rstudio/logging.conf
+                """,
+            ),
            (
                "${NB_USER}",
                # Install a pinned version of devtools, IRKernel and shiny
--- a/repo2docker/contentproviders/base.py
+++ b/repo2docker/contentproviders/base.py
@ -4,6 +4,7 @@ Base classes for repo2docker ContentProviders
 ContentProviders accept a `spec` of various kinds, and
 provide the contents from the spec to a given output directory.
 """
+
 import logging
 import os

--- a/repo2docker/contentproviders/dataverse.json
+++ b/repo2docker/contentproviders/dataverse.json
@ -639,16 +639,42 @@
        },
        {
            "description": "The Research Data Repository for the Max Planck Society.",
-            "full_name": "Edmond - Research Data Repository for the Max Planck Society",
+            "full_name": "Edmond - Research Data Repository for the Max Planck Society (old domain)",
            "id": 1795,
            "is_active": true,
            "lat": 48.1366,
            "lng": 11.5771,
            "logo": "https://edmond.mpdl.mpg.de/logos/navbar/logo_for_bright.png",
-            "name": "Edmond",
-            "slug": "",
+            "name": "Edmond (old domain)",
+            "slug": "edmond_mpdl_mpg_de",
            "url": "https://edmond.mpdl.mpg.de",
-            "version": "5.10"
+            "version": "5.14"
+        },
+        {
+            "description": "The Research Data Repository for the Max Planck Society.",
+            "full_name": "Edmond - Research Data Repository for the Max Planck Society",
+            "id": 1796,
+            "is_active": true,
+            "lat": 48.1366,
+            "lng": 11.5771,
+            "logo": "https://edmond.mpg.de/logos/navbar/logo_for_bright.png",
+            "name": "Edmond",
+            "slug": "edmond_mpg_de",
+            "url": "https://edmond.mpg.de",
+            "version": "5.14"
+        },
+        {
+            "description": "The institutional research data repository of the National Yang Ming Chiao Tung University",
+            "full_name": "National Yang Ming Chiao Tung University",
+            "id": 1797,
+            "is_active": true,
+            "lat": 24.7867714,
+            "lng": 120.9984256,
+            "logo": "https://dataverse.lib.nycu.edu.tw/logos/navbar/logo.png",
+            "name": "NYCU Dataverse",
+            "slug": "nycu-dataverse",
+            "url": "https://dataverse.lib.nycu.edu.tw",
+            "version": "5.10.1"
        }        
    ]
 }
--- a/repo2docker/contentproviders/doi.py
+++ b/repo2docker/contentproviders/doi.py
@ -51,9 +51,15 @@ class DoiProvider(ContentProvider):
            try:
                resp = self._request(f"https://doi.org/{doi}")
                resp.raise_for_status()
-            # If the DOI doesn't resolve, just return URL
-            except HTTPError:
-                return doi
+            except HTTPError as e:
+                # If the DOI doesn't exist, just return URL
+                if e.response.status_code == 404:
+                    return doi
+                # Reraise any other errors because if the DOI service is down (or
+                # we hit a rate limit) we don't want to silently continue to the
+                # default Git provider as this leads to a misleading error.
+                logging.error(f"DOI {doi} does not resolve: {e}")
+                raise
            return resp.url
        else:
            # Just return what is actulally just a URL
--- a/repo2docker/contentproviders/zenodo.py
+++ b/repo2docker/contentproviders/zenodo.py
@ -22,19 +22,26 @@ class Zenodo(DoiProvider):
                "hostname": [
                    "https://sandbox.zenodo.org/record/",
                    "http://sandbox.zenodo.org/record/",
+                    "http://sandbox.zenodo.org/records/",
                ],
                "api": "https://sandbox.zenodo.org/api/records/",
-                "filepath": "files",
-                "filename": "filename",
-                "download": "links.download",
+                "files": "links.files",
+                "filepath": "entries",
+                "filename": "key",
+                "download": "links.content",
                "type": "metadata.upload_type",
            },
            {
-                "hostname": ["https://zenodo.org/record/", "http://zenodo.org/record/"],
+                "hostname": [
+                    "https://zenodo.org/record/",
+                    "http://zenodo.org/record/",
+                    "https://zenodo.org/records/",
+                ],
                "api": "https://zenodo.org/api/records/",
-                "filepath": "files",
-                "filename": "filename",
-                "download": "links.download",
+                "files": "links.files",
+                "filepath": "entries",
+                "filename": "key",
+                "download": "links.content",
                "type": "metadata.upload_type",
            },
            {
@ -43,6 +50,7 @@ class Zenodo(DoiProvider):
                    "http://data.caltech.edu/records/",
                ],
                "api": "https://data.caltech.edu/api/record/",
+                "files": "",
                "filepath": "metadata.electronic_location_and_access",
                "filename": "electronic_name.0",
                "download": "uniform_resource_identifier",
@ -69,9 +77,17 @@ class Zenodo(DoiProvider):
            f'{host["api"]}{record_id}',
            headers={"accept": "application/json"},
        )
-
        record = resp.json()

+        if host["files"]:
+            yield f"Fetching Zenodo record {record_id} files.\n"
+            files_url = deep_get(record, host["files"])
+            resp = self.urlopen(
+                files_url,
+                headers={"accept": "application/json"},
+            )
+            record = resp.json()
+
        files = deep_get(record, host["filepath"])
        only_one_file = len(files) == 1
        for file_ref in files:
--- a/repo2docker/semver.py
+++ b/repo2docker/semver.py
@ -10,7 +10,6 @@ matcher functors take a version string and return True if it passes its
 constraints.
 """

-
 import re
 from functools import lru_cache

--- a/tests/conda/py35-binder-dir/verify
+++ b/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 == "1.4.0", out
+assert out == "1.5.7", out

 out = sh(["mamba", "--version"])
 assert (
    out
-    == """mamba 1.4.0
-conda 23.1.0"""
+    == """mamba 1.5.7
+conda 24.3.0"""
 ), out

 sh([kernel_python, "-c", "import numpy"])
--- a/tests/conftest.py
+++ b/tests/conftest.py
@ -33,11 +33,11 @@ from repo2docker.__main__ import make_r2d
 TESTS_DIR = os.path.abspath(os.path.dirname(__file__))


-def pytest_collect_file(parent, path):
-    if path.basename == "verify":
-        return LocalRepo.from_parent(parent, fspath=path)
-    elif path.basename.endswith(".repos.yaml"):
-        return RemoteRepoList.from_parent(parent, fspath=path)
+def pytest_collect_file(parent, file_path):
+    if file_path.name == "verify":
+        return LocalRepo.from_parent(parent, path=file_path)
+    elif file_path.name.endswith(".repos.yaml"):
+        return RemoteRepoList.from_parent(parent, path=file_path)


 def make_test_func(args, skip_build=False, extra_run_kwargs=None):
@ -105,7 +105,7 @@ def base_image():
    """
    Base ubuntu image to use when testing specific BuildPacks
    """
-    return "buildpack-deps:bionic"
+    return "buildpack-deps:jammy"


 def _add_content_to_git(repo_dir):
@ -213,7 +213,7 @@ class Repo2DockerTest(pytest.Function):
        super().__init__(name, parent, callobj=f)

    def reportinfo(self):
-        return (self.parent.fspath, None, "")
+        return (self.parent.path, None, "")

    def repr_failure(self, excinfo):
        err = excinfo.value
@ -233,24 +233,23 @@ class LocalRepo(pytest.File):
        args = ["--appendix", 'RUN echo "appendix" > /tmp/appendix']
        # If there's an extra-args.yaml file in a test dir, assume it contains
        # a yaml list with extra arguments to be passed to repo2docker
-        extra_args_path = os.path.join(self.fspath.dirname, "test-extra-args.yaml")
-        if os.path.exists(extra_args_path):
-            with open(extra_args_path) as f:
-                extra_args = yaml.safe_load(f)
+        extra_args_path = self.path.parent / "test-extra-args.yaml"
+        if extra_args_path.exists():
+            extra_args = yaml.safe_load(extra_args_path.read_text())
            args += extra_args

-        print(self.fspath.basename, self.fspath.dirname, str(self.fspath))
+        print(self.path.name, self.path.parent, str(self.path))
        # re-use image name for multiple tests of the same image
        # so we don't run through the build twice
-        rel_repo_dir = os.path.relpath(self.fspath.dirname, TESTS_DIR)
+        rel_repo_dir = os.path.relpath(self.path.parent, TESTS_DIR)
        image_name = f"r2d-tests-{escapism.escape(rel_repo_dir, escape_char='-').lower()}-{int(time.time())}"
        args.append(f"--image-name={image_name}")
-        args.append(self.fspath.dirname)
+        args.append(str(self.path.parent))
        yield Repo2DockerTest.from_parent(self, name="build", args=args)

        yield Repo2DockerTest.from_parent(
            self,
-            name=self.fspath.basename,
+            name=self.path.name,
            args=args + ["./verify"],
            skip_build=True,
        )
@ -273,7 +272,7 @@ class LocalRepo(pytest.File):

 class RemoteRepoList(pytest.File):
    def collect(self):
-        with self.fspath.open() as f:
+        with self.path.open() as f:
            repos = yaml.safe_load(f)
        for repo in repos:
            args = []
--- a/tests/unit/contentproviders/test_doi.py
+++ b/tests/unit/contentproviders/test_doi.py
@ -30,8 +30,14 @@ def test_url_headers(requests_mock):
    assert result.request.headers["User-Agent"] == f"repo2docker {__version__}"


-def test_unresolving_doi():
+@pytest.mark.parametrize(
+    "requested_doi, expected",
+    [
+        ("10.5281/zenodo.3242074", "https://zenodo.org/records/3242074"),
+        # Unresolving DOI:
+        ("10.1/1234", "10.1/1234"),
+    ],
+)
+def test_doi2url(requested_doi, expected):
    doi = DoiProvider()
-
-    fakedoi = "10.1/1234"
-    assert doi.doi2url(fakedoi) is fakedoi
+    assert doi.doi2url(requested_doi) == expected
--- a/tests/unit/contentproviders/test_zenodo.py
+++ b/tests/unit/contentproviders/test_zenodo.py
@ -92,16 +92,31 @@ def test_fetch_software_from_github_archive(requests_mock):
    # we "fetch" a local ZIP file to simulate a Zenodo record created from a
    # GitHub repository via the Zenodo-GitHub integration
    with zenodo_archive() as zen_path:
-        mock_response = {
+        mock_record = {
            "files": [
                {
                    "filename": "some_dir/afake.zip",
-                    "links": {"download": f"file://{zen_path}"},
                }
            ],
+            "links": {
+                "files": "https://zenodo.org/api/records/1234/files",
+            },
            "metadata": {"upload_type": "other"},
        }
-        requests_mock.get("https://zenodo.org/api/records/1234", json=mock_response)
+        requests_mock.get("https://zenodo.org/api/records/1234", json=mock_record)
+
+        mock_record_files = {
+            "entries": [
+                {
+                    "key": "some_dir/afake.zip",
+                    "links": {"content": f"file://{zen_path}"},
+                }
+            ],
+        }
+        requests_mock.get(
+            "https://zenodo.org/api/records/1234/files", json=mock_record_files
+        )
+
        requests_mock.get(f"file://{zen_path}", content=open(zen_path, "rb").read())

        zen = Zenodo()
@ -121,18 +136,33 @@ def test_fetch_software(requests_mock):
    # we "fetch" a local ZIP file to simulate a Zenodo software record with a
    # ZIP file in it
    with zenodo_archive() as zen_path:
-        mock_response = {
+        mock_record = {
            "files": [
                {
                    # this is the difference to the GitHub generated one,
                    # the ZIP file isn't in a directory
                    "filename": "afake.zip",
-                    "links": {"download": f"file://{zen_path}"},
                }
            ],
+            "links": {
+                "files": "https://zenodo.org/api/records/1234/files",
+            },
            "metadata": {"upload_type": "software"},
        }
-        requests_mock.get("https://zenodo.org/api/records/1234", json=mock_response)
+        requests_mock.get("https://zenodo.org/api/records/1234", json=mock_record)
+
+        mock_record_files = {
+            "entries": [
+                {
+                    "key": "afake.zip",
+                    "links": {"content": f"file://{zen_path}"},
+                }
+            ],
+        }
+        requests_mock.get(
+            "https://zenodo.org/api/records/1234/files", json=mock_record_files
+        )
+
        requests_mock.get(f"file://{zen_path}", content=open(zen_path, "rb").read())

        with TemporaryDirectory() as d:
@ -151,20 +181,38 @@ def test_fetch_data(requests_mock):
    # we "fetch" a local ZIP file to simulate a Zenodo data record
    with zenodo_archive() as a_zen_path:
        with zenodo_archive() as b_zen_path:
-            mock_response = {
+            mock_record = {
                "files": [
                    {
                        "filename": "afake.zip",
-                        "links": {"download": f"file://{a_zen_path}"},
                    },
                    {
                        "filename": "bfake.zip",
-                        "links": {"download": f"file://{b_zen_path}"},
                    },
                ],
+                "links": {
+                    "files": "https://zenodo.org/api/records/1234/files",
+                },
                "metadata": {"upload_type": "data"},
            }
-            requests_mock.get("https://zenodo.org/api/records/1234", json=mock_response)
+            requests_mock.get("https://zenodo.org/api/records/1234", json=mock_record)
+
+            mock_record_files = {
+                "entries": [
+                    {
+                        "key": "afake.zip",
+                        "links": {"content": f"file://{a_zen_path}"},
+                    },
+                    {
+                        "key": "bfake.zip",
+                        "links": {"content": f"file://{b_zen_path}"},
+                    },
+                ],
+            }
+            requests_mock.get(
+                "https://zenodo.org/api/records/1234/files", json=mock_record_files
+            )
+
            requests_mock.get(
                f"file://{a_zen_path}", content=open(a_zen_path, "rb").read()
            )
--- a/tests/unit/test_args.py
+++ b/tests/unit/test_args.py
@ -1,6 +1,7 @@
 """
 Test argument parsing and r2d construction
 """
+
 import os

 import pytest
--- a/tests/unit/test_clone_depth.py
+++ b/tests/unit/test_clone_depth.py
@ -6,6 +6,7 @@ container requires a specific repository and commit to be checked out,
 and that is the only thing that is tested.

 """
+
 import os
 import subprocess
 from tempfile import TemporaryDirectory
--- a/tests/unit/test_connect_url.py
+++ b/tests/unit/test_connect_url.py
@ -1,6 +1,7 @@
 """
 Test if the explict hostname is supplied correctly to the container
 """
+
 import time

 import requests
--- a/tests/unit/test_env.py
+++ b/tests/unit/test_env.py
@ -1,6 +1,7 @@
 """
 Test that environment variables may be defined
 """
+
 import os
 import subprocess
 import sys
--- a/tests/unit/test_external_scripts.py
+++ b/tests/unit/test_external_scripts.py
@ -1,4 +1,5 @@
 """Test if assemble scripts from outside of r2d repo are accepted."""
+
 import time

 from repo2docker.app import Repo2Docker
--- a/tests/unit/test_labels.py
+++ b/tests/unit/test_labels.py
@ -1,6 +1,7 @@
 """
 Test if labels are supplied correctly to the container
 """
+
 from unittest.mock import Mock

 import pytest
--- a/tests/unit/test_subdir.py
+++ b/tests/unit/test_subdir.py
@ -1,6 +1,7 @@
 """
 Test if the subdirectory is correctly navigated to
 """
+
 import os

 import escapism
--- a/tests/unit/test_users.py
+++ b/tests/unit/test_users.py
@ -1,6 +1,7 @@
 """
 Test that User name and ID mapping works
 """
+
 import os
 import subprocess
 import tempfile
--- a/tests/unit/test_utils.py
+++ b/tests/unit/test_utils.py
@ -1,6 +1,7 @@
 """
 Tests for repo2docker/utils.py
 """
+
 import os
 import platform
 import subprocess
--- a/tests/venv/binder-dir/.containerignore
+++ b/tests/venv/binder-dir/.containerignore
@ -0,0 +1 @@
+binder/
--- a/tests/venv/binder-dir/.dockerignore
+++ b/tests/venv/binder-dir/.dockerignore
@ -0,0 +1 @@
+binder/
--- a/versioneer.py
+++ b/versioneer.py
Autor	SHA1	Wiadomość	Data
Erik Sundell	af6d3e8448	Merge pull request #1344 from jupyterhub/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate	2024-05-07 07:39:29 +02:00
pre-commit-ci[bot]	3c204f3b08	[pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 24.3.0 → 24.4.2](https://github.com/psf/black/compare/24.3.0...24.4.2)	2024-05-06 22:03:34 +00:00
Erik Sundell	d2f467cef6	Merge pull request #1342 from jupyterhub/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate	2024-04-02 09:54:26 +02:00
pre-commit-ci[bot]	0e7907f86b	[pre-commit.ci] pre-commit autoupdate updates: - [github.com/asottile/pyupgrade: v3.15.0 → v3.15.2](https://github.com/asottile/pyupgrade/compare/v3.15.0...v3.15.2) - [github.com/psf/black: 24.1.1 → 24.3.0](https://github.com/psf/black/compare/24.1.1...24.3.0)	2024-04-01 22:10:42 +00:00
Simon Li	243669b928	Merge pull request #1341 from manics/changelog-2024.03.0 Changelog for 2024.03.0	2024-03-31 20:43:31 +02:00
Simon Li	d4bb9c14da	Changelog for 2024.03.0	2024-03-28 19:13:23 +00:00
Erik Sundell	f667caf49c	Merge pull request #1332 from yuvipanda/bump-alpine Dockerfile: bump alpine from 3.17 to 3.19 and Python 3.10 to 3.11	2024-03-24 23:08:31 +01:00
Erik Sundell	755a32bc2a	Merge pull request #1337 from SylvainCorlay/mamba-1.5.7 Update mamba to 1.5.7 from 1.5.1, and conda to 24.3.0 from 23.7.4	2024-03-24 22:50:58 +01:00
Erik Sundell	91d3f150e5	Use ARG instead of ENV for build time only environment variable	2024-03-24 22:35:15 +01:00
Erik Sundell	f121a0d481	Use modern ENV syntax in Dockerfile The use of `ENV key value` is an old alternative syntax still around for backward compatibility, but may be removed according to https://docs.docker.com/reference/dockerfile/#env.	2024-03-24 22:22:47 +01:00
Erik Sundell	57e4b3f687	Fix unrelated comment	2024-03-24 22:18:23 +01:00
Erik Sundell	920ddd86ac	Update conda from 23.7.4 to 24.3.0	2024-03-24 22:16:05 +01:00
YuviPanda	601fa25291	Don't use --user to install anything	2024-03-22 19:40:41 -07:00
YuviPanda	756e7d1a98	Put everything inside a venv	2024-03-22 19:40:41 -07:00
YuviPanda	dd9f6ad2de	Bump alpine version used in Dockerfile Brings us to latest alpine, and to a newer python	2024-03-22 19:40:41 -07:00
Sylvain Corlay	01d818b974	Update to mamba 1.5.7	2024-03-22 21:34:50 +01:00
Erik Sundell	a20dd1cf97	Merge pull request #1333 from jupyterhub/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate	2024-02-06 08:22:46 +01:00
pre-commit-ci[bot]	f2c1cb7a8c	[pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci	2024-02-05 20:28:56 +00:00
pre-commit-ci[bot]	625b296773	[pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 23.12.1 → 24.1.1](https://github.com/psf/black/compare/23.12.1...24.1.1)	2024-02-05 20:26:53 +00:00
Yuvi Panda	3221560bb1	Merge pull request #1330 from manics/pin-pytest Support pytest=8	2024-02-01 16:41:55 -08:00
Simon Li	56299a2312	Don't pin upper pytest version	2024-02-01 22:39:08 +00:00
Erik Sundell	c806c1c1c2	Merge pull request #1331 from jupyterhub/dependabot/github_actions/codecov/codecov-action-4 build(deps): bump codecov/codecov-action from 3 to 4	2024-02-01 10:29:49 +01:00
dependabot[bot]	767047c84c	build(deps): bump codecov/codecov-action from 3 to 4 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>	2024-02-01 05:06:50 +00:00
Simon Li	237375f3a4	pytest >=7,<9	2024-01-28 19:26:24 +00:00
Simon Li	6fe9ee6763	pytest: replace fspath with path	2024-01-28 18:04:51 +00:00
Simon Li	6f92fa0e84	Merge pull request #1329 from TimoRoth/update_versioneer Update versioneer	2024-01-28 17:07:02 +00:00
Simon Li	3505ad7c8b	Pin pytest<8	2024-01-28 17:00:51 +00:00
pre-commit-ci[bot]	089e919e19	[pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci	2024-01-28 14:02:27 +00:00
Timo Rothenpieler	fa8394b09b	Run pre-commit	2024-01-28 15:02:03 +01:00
Timo Rothenpieler	2eac520042	Update versioneer	2024-01-27 15:36:11 +01:00
Min RK	6aad2bcce2	Merge pull request #1205 from sgaist/implement_dockerignore_support Implement support for dockerignore and containerignore	2024-01-24 11:39:22 +01:00
Yuvi Panda	b3b8db7954	Merge pull request #1326 from twtw/addnycu Add NYCU Dataverse	2024-01-19 19:44:36 -08:00
Yuvi Panda	8f0d9aaf9e	Merge pull request #1318 from hiroyuki-sato/topic/add-example [MRG] docs: Add base_image parameter example.	2024-01-19 18:51:34 -08:00
Yuvi Panda	abe7c15b3a	Merge branch 'main' into addnycu	2024-01-19 18:50:35 -08:00
Samuel Gaist	77df191536	test(venv): add ignore files above binderdir This ensures that the ignore files are retrieved from the proper folder. If they weren't the build would not succeed as the binder folder is ignored.	2024-01-19 08:45:06 +00:00
Samuel Gaist	09e503c4e6	feat: respect the root folder configured when looking for ignore files See the design chapter for more details.	2024-01-19 08:45:06 +00:00
Samuel Gaist	a51235f9a5	fix: remove the ignore .git folder default when no exclude files are present	2024-01-19 08:45:06 +00:00
Samuel Gaist	d6670f4378	refactor: use list comprehension rather filter+lambda	2024-01-19 08:45:06 +00:00
Samuel Gaist	3028d07182	fix: create src directory in any case The original behavior was to create an src directory with the content of the repository. The creation would happen in any case (remote or local repository). With the filtering in place and the default to remove the .git folder, it breaks the build as the src folder can be missing. This patch ensures that the directory is present in the tar so the build can continue as it did until now.	2024-01-19 08:45:06 +00:00
Samuel Gaist	6b8b2334e7	feat: implement support for dockerignore and containerignore Currently repo2docker creates a context object that includes the whole content of the repository it builds an image for. Thus it includes folders like .git which is usually something that has no interest in the final image, can take quite a lot of space and most importantly, kills the caching of that layer. This patch adds support for reading dockerignore and containerignore files that are used to ensure only the relevant data are used to build the image. By default it also excludes the .git folder if neither of these files are provided.	2024-01-19 08:45:06 +00:00
Simon Li	0e02889faf	Merge pull request #1321 from MPDL/MPDL_Dataverse New domain for Edmond MPG repository	2024-01-18 20:56:57 +00:00
Erik Sundell	7713f2a82f	Merge pull request #1327 from jupyterhub/dependabot/github_actions/actions/upload-artifact-4 build(deps): bump actions/upload-artifact from 3 to 4	2024-01-04 01:15:54 +01:00
Erik Sundell	40682d762a	Merge pull request #1322 from jupyterhub/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate	2024-01-04 01:04:55 +01:00
Erik Sundell	809f511799	Merge pull request #1328 from jupyterhub/dependabot/github_actions/actions/setup-python-5 build(deps): bump actions/setup-python from 4 to 5	2024-01-04 00:50:08 +01:00
pre-commit-ci[bot]	97ce87c079	[pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 23.10.1 → 23.12.1](https://github.com/psf/black/compare/23.10.1...23.12.1) - [github.com/pycqa/isort: 5.12.0 → 5.13.2](https://github.com/pycqa/isort/compare/5.12.0...5.13.2) - [github.com/pre-commit/mirrors-prettier: v3.0.3 → v4.0.0-alpha.8](https://github.com/pre-commit/mirrors-prettier/compare/v3.0.3...v4.0.0-alpha.8)	2024-01-01 20:22:43 +00:00
dependabot[bot]	6dc8dee823	build(deps): bump actions/setup-python from 4 to 5 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>	2024-01-01 05:09:55 +00:00
dependabot[bot]	766f4b8eb4	build(deps): bump actions/upload-artifact from 3 to 4 Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3 to 4. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>	2024-01-01 05:09:51 +00:00
Cheng-Yen Liu	066e951a7d	Add NYCU Dataverse	2023-12-27 03:28:08 +08:00
haarli	38f6e0acd1	Logo URL	2023-11-10 10:47:13 +01:00
haarli	24fa50118e	New domain for Edmond MPG repository	2023-11-10 09:56:57 +01:00
Min RK	c6f97e55c1	Merge pull request #1319 from jupyterhub/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate	2023-11-07 10:03:02 +01:00
pre-commit-ci[bot]	42ffce107d	[pre-commit.ci] pre-commit autoupdate updates: - [github.com/asottile/pyupgrade: v3.14.0 → v3.15.0](https://github.com/asottile/pyupgrade/compare/v3.14.0...v3.15.0) - [github.com/psf/black: 23.9.1 → 23.10.1](https://github.com/psf/black/compare/23.9.1...23.10.1)	2023-11-06 20:27:49 +00:00
Hiroyuki Sato	570c11769b	docs: Add base_image parameter example. Some users don't know how to set base_image. Add an example of how to set it.	2023-10-24 21:45:01 +09:00
Erik Sundell	57d229eb19	Merge pull request #1317 from manics/rstudio-logging rstudio: log-level info to stderr	2023-10-23 00:21:44 +02:00
Simon Li	72cfc12a8d	rstudio: log-level info to stderr	2023-10-22 19:20:16 +01:00
Yuvi Panda	8bdf681a4a	Merge pull request #1313 from manics/upgrade-mamba Upgrade mamba and refreeze	2023-10-19 12:19:26 +05:30
Simon Li	f4591425b4	Fix mamba/conda version test	2023-10-19 10:46:13 +05:30
Simon Li	4b0c7d9bfd	conda 23.7.4 error libmamba Could not solve for environment specs The following packages are incompatible ├─ conda 23.9.0 is requested and can be installed; └─ mamba 1.5.1 is not installable because it requires └─ conda >=4.14,<23.9.0a0 , which conflicts with any installable versions previously reported.	2023-10-19 10:46:13 +05:30
Simon Li	2e26e773b7	./freeze.py	2023-10-19 10:46:13 +05:30
Simon Li	3ec7d41bce	mamba 1.5.1 conda 23.9.0	2023-10-19 10:46:13 +05:30
Yuvi Panda	aa57e01d24	Merge pull request #1315 from manics/zenodo Get Zenodo working again	2023-10-19 10:45:09 +05:30
Simon Li	fc7de2768b	Zenodo DOI now returning https://zenodo.org/records/ instead of https://zenodo.org/record/	2023-10-15 21:17:51 +01:00
Simon Li	1fc8f192ee	doi2url: Don't ignore non-404 errors	2023-10-15 17:17:59 +01:00
Simon Li	ebdd121b05	Update zenodo mocks	2023-10-15 17:17:59 +01:00
Simon Li	74a94cf2b0	Test resolving DOI This helps distinguish temporary(?) errors in the DOI resolution from errors in the content provider	2023-10-15 17:17:55 +01:00
Simon Li	efb4cd3bbc	Attempt to fix Zenodo Done by inspecting API responses - https://zenodo.org/api/records/3242074 - https://zenodo.org/api/records/3242074/files	2023-10-15 13:43:15 +01:00
Yuvi Panda	de496f893b	Merge pull request #1309 from manics/upgrade-guide-ubuntu2204 Add Ubuntu 22.04 upgrade guide	2023-10-15 10:08:39 +05:30
Simon Li	2ad8eebd41	ubuntu 18.04: warn about r2d build being frozen in time	2023-10-13 00:14:25 +01:00
Yuvi Panda	8c32db9987	Merge pull request #1310 from yuvipanda/rsession r: Bump version of rsession-proxy	2023-10-12 15:29:19 +00:00
YuviPanda	18ab230b0c	Bump rsession-proxy pin instead We can move to a proper pinning setup later	2023-10-12 07:49:13 -07:00
YuviPanda	654199c705	r: Don't strictly pin version of rsession-proxy If memory serves me right, the specific version semantics were here because at some point we were installing different versions of rsession-proxy for different versions of R. We don't do that anymore, so we should just unpin it and let the pip solver install the appropriate version. Hopefully fixes https://discourse.jupyter.org/t/r-conda-example-repo-isnt-working-any-more/21739/3	2023-10-12 06:59:45 -07:00
Simon Li	94a0043883	upgrade: Link dockerfile	2023-10-08 15:52:46 +01:00
Simon Li	8f0d763ec4	Add Ubuntu 22.04 upgrade guide	2023-10-08 15:46:22 +01:00
Erik Sundell	d0ad8d3715	Merge pull request #1291 from jupyterhub/pre-commit-ci-update-config [pre-commit.ci] pre-commit autoupdate	2023-10-03 12:41:11 +02:00
pre-commit-ci[bot]	714a26e11d	[pre-commit.ci] pre-commit autoupdate updates: - [github.com/asottile/pyupgrade: v3.4.0 → v3.14.0](https://github.com/asottile/pyupgrade/compare/v3.4.0...v3.14.0) - [github.com/psf/black: 23.3.0 → 23.9.1](https://github.com/psf/black/compare/23.3.0...23.9.1) - [github.com/pre-commit/mirrors-prettier: v3.0.0-alpha.9-for-vscode → v3.0.3](https://github.com/pre-commit/mirrors-prettier/compare/v3.0.0-alpha.9-for-vscode...v3.0.3)	2023-10-03 10:35:34 +00:00
Erik Sundell	129f624120	Merge pull request #1307 from jupyterhub/dependabot/github_actions/docker/build-push-action-5 build(deps): bump docker/build-push-action from 4 to 5	2023-10-02 12:18:48 +02:00
dependabot[bot]	77289c4719	build(deps): bump docker/build-push-action from 4 to 5 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4 to 5. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/v4...v5) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>	2023-10-01 08:52:37 +00:00
Erik Sundell	4cd89f5328	Merge pull request #1306 from jupyterhub/dependabot/github_actions/docker/setup-qemu-action-3 build(deps): bump docker/setup-qemu-action from 2 to 3	2023-10-01 10:52:04 +02:00
dependabot[bot]	8ee344ef30	build(deps): bump docker/setup-qemu-action from 2 to 3 Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2 to 3. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](https://github.com/docker/setup-qemu-action/compare/v2...v3) --- updated-dependencies: - dependency-name: docker/setup-qemu-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>	2023-10-01 08:26:04 +00:00
Erik Sundell	580101abd9	Merge pull request #1305 from jupyterhub/dependabot/github_actions/docker/setup-buildx-action-3 build(deps): bump docker/setup-buildx-action from 2 to 3	2023-10-01 10:25:21 +02:00
Erik Sundell	2d82547742	Merge pull request #1308 from jupyterhub/dependabot/github_actions/actions/checkout-4 build(deps): bump actions/checkout from 3 to 4	2023-10-01 10:20:21 +02:00
dependabot[bot]	c7d5094e06	build(deps): bump actions/checkout from 3 to 4 Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>	2023-10-01 05:27:30 +00:00
dependabot[bot]	df22b13f94	build(deps): bump docker/setup-buildx-action from 2 to 3 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2 to 3. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/v2...v3) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>	2023-10-01 05:27:20 +00:00
Erik Sundell	3fe6c75a88	Merge pull request #1287 from yuvipanda/bump Upgrade base image from to Ubuntu 22.04 from 18.04	2023-09-18 11:53:35 +02:00
Erik Sundell	c53971b1b5	docs: fix outdated reference to ubuntu:bionic	2023-08-08 12:24:41 +02:00
Simon Li	d414e994fc	Merge pull request #1299 from SylvainCorlay/update-mamba-1.4.9 Update conda and mamba	2023-07-18 16:12:28 +01:00
Sylvain Corlay	fbe7ebad53	Update conda and mamba	2023-07-18 12:06:16 +01:00
Yuvi Panda	df111a06ee	Merge pull request #1293 from yamaton/fix-install-rstudio Fix rstudio-build selection	2023-07-14 09:34:10 -07:00
Simon Li	e0609adca8	Merge pull request #1294 from fcollonval/patch-2 Point to official documentation for handling JupyterLab workspace	2023-07-12 18:45:05 +01:00
Frédéric Collonval	e231c1a619	Point to official documentation for handling JupyterLab workspace	2023-07-11 13:16:17 +02:00
Yamato Matsuoka	6a0d76a308	Fix rstudio-build selection	2023-07-08 12:50:12 -04:00
Min RK	247e9535b1	Merge pull request #1288 from yuvipanda/r-docs Update version of R available	2023-06-13 13:49:38 +02:00
YuviPanda	0205c112b9	Update version of R available Fixes https://github.com/jupyterhub/repo2docker/issues/1278	2023-06-13 10:40:48 +02:00
YuviPanda	e586b26110	Upgrade base image to Ubuntu 22.04 18.04 was EOL May 2023, with only paid support now available (https://ubuntu.com/blog/18-04-end-of-standard-support). Let's bump the default base image to 22.04. This might break some repos that have apt.txt based packages, but I don't really think there's a way around that. If specific package pinning is needed, users unfortunately need to use a Dockerfile. Ref https://github.com/jupyterhub/repo2docker/issues/1258	2023-06-13 13:03:05 +05:30