========= Changelog ========= Version 2022.10.0 ================= `Full changelog `__ New features ------------ - Update Jupyter dependencies :pr:`1193` by :user:`jtpio` - add Python 3.10 base environment :pr:`1175` by :user:`minrk` - Bump default R version to 4.2 from 4.1, and let R 3.4 go from 3.4.0 to 3.4.4 :pr:`1165` by :user:`yuvipanda` - Support pulling from zenodo sandbox too :pr:`1169` by :user:`yuvipanda` - Add MPDL Dataverse :pr:`1167` by :user:`wilhelmfrank` - Add JPL Dataverse :pr:`1163` by :user:`foobarbecue` - upgrade RStudio Server to v2022.02.1 :pr:`1148` by :user:`aplamada` - Pass build_args to `render()` during `--no-build` for consistency with regular builds :pr:`1135` by :user:`yoogottamk` Documentation improvements -------------------------- - Update 'how to get R' section :pr:`1147` by :user:`yuvipanda` - Post release fixes :pr:`1133` by :user:`manics` API changes ----------- Bug fixes --------- - consistent log handling when not using JSON loggers :pr:`1177` by :user:`minrk` - Fix Read-Only filesystem permission issue for log file :pr:`1156` by :user:`timeu` - handle permission issue writing .jupyter-server-log.txt in REPO_DIR :pr:`1151` by :user:`pymonger` - handle r version being unspecified in environment.yml :pr:`1141` by :user:`minrk` Other merged PRs ---------------- - Remove conda buildpacks pin of r-irkernel to 1.2 :pr:`1191` by :user:`consideRatio` - ci: refactor julia/r/conda tests - now ~25 min instead of ~50 min :pr:`1188` by :user:`consideRatio` - ci: general refresh of github workflows, update gha versions and let dependabot do it, etc. :pr:`1186` by :user:`consideRatio` - Use enum to standardise `phase` :pr:`1185` by :user:`manics` - fail on unsupported Python :pr:`1184` by :user:`minrk` - mount wheels from build stage instead of copying them :pr:`1182` by :user:`minrk` - get CI working again :pr:`1178` by :user:`minrk` - explicitly build linux/amd64 images :pr:`1176` by :user:`minrk` - Freeze.py update :pr:`1173` by :user:`manics` - Bump version of nodejs :pr:`1172` by :user:`yuvipanda` - Update mamba :pr:`1171` by :user:`SylvainCorlay` - ci: switch to using a 2fa enabled accounts pypi api-token :pr:`1166` by :user:`consideRatio` - Get R from RStudio provided apt packages (.deb files) :pr:`1161` by :user:`yuvipanda` - Shallow clone HEAD :pr:`1160` by :user:`daradib` - Update black version :pr:`1150` by :user:`yuvipanda` - Update base notebook packages :pr:`1149` by :user:`yuvipanda` - Update Dockerfile to current Alpine (ALPINE_VERSION=3.15.0) :pr:`1136` by :user:`holzman` - update Python in some dockerfile tests :pr:`1130` by :user:`minrk` Version 2022.02.0 ================= `Full changelog `__ New features ------------ - Update ipywidgets jupyter-offlinenotebook jupyterlab :pr:`1127` by :user:`manics` - Allow passing in extra args to Docker initialization :pr:`1124` by :user:`yuvipanda` - Allow passing in traitlets via commandline :pr:`1123` by :user:`yuvipanda` - Bump default R version to 4.1 :pr:`1107` by :user:`yuvipanda` - Update jupyterlab 3.2.5 jupyter-resource-usage 0.6.1 :pr:`1105` by :user:`manics` - Get binary R packages from packagemanager.rstudio.com :pr:`1104` by :user:`yuvipanda` - Support R 4.1 :pr:`1102` by :user:`yuvipanda` - Add command line option to pass extra build args :pr:`1100` by :user:`TimoRoth` - Set labels when building image from Dockerfile :pr:`1097` by :user:`TimoRoth` - jupyterlab 3.1.17 :pr:`1092` by :user:`minrk` - Bump JupyterLab to 3.1.11 :pr:`1081` by :user:`choldgraf` - Bootstrap base env with micromamba :pr:`1062` by :user:`wolfv` - Default UI to JupyterLab :pr:`1035` by :user:`SylvainCorlay` API changes ----------- Bug fixes --------- Other merged PRs ---------------- - Put micromamba in /usr/local/bin and use mamba for installs :pr:`1128` by :user:`minrk` - Remove deprecated calls to distutils :pr:`1122` by :user:`minrk` - Delete /tmp/downloaded_packages after running install.R :pr:`1119` by :user:`yuvipanda` - Use a smaller R library in our tests :pr:`1118` by :user:`yuvipanda` - Only get R itself (r-base-core) from apt, not CRAN packages :pr:`1117` by :user:`minrk` - set USER root after each directive block :pr:`1115` by :user:`minrk` - Say 'apt repository' rather than PPA :pr:`1111` by :user:`yuvipanda` - add tests for R conda :pr:`1108` by :user:`aplamada` - Add help message to freeze.py :pr:`1106` by :user:`manics` - Quieter R builds :pr:`1103` by :user:`yuvipanda` - update user_interface doc to reflect that lab is default :pr:`1085` by :user:`minrk` - Updates to dev docs + Recommonmark -> MyST Parser :pr:`1082` by :user:`choldgraf` - Fix Docker build (again) :pr:`1078` by :user:`manics` - [mrg] __init__.py: r_version: fixed description :pr:`1074` by :user:`magnush0lm` - Typo fix in utils docstring :pr:`1072` by :user:`jgarte` - Rename requirements.py-3.5.txt to requirements.py-3.5.pip :pr:`1061` by :user:`manics` - Remove nodesource' nodejs :pr:`847` by :user:`yuvipanda` Version 2021.08.0 ================= `Full changelog `__ The repo2docker container image has moved to `quay.io/jupyterhub/repo2docker `_ New features ------------ - always unpack a single zenodo zip :pr:`1043` by :user:`akhmerov` - Refreeze with conda-lock :pr:`1024` by :user:`minrk` - Refine buffered output debugging :pr:`1016` by :user:`minrk` - reimplement entrypoint in Python :pr:`1014` by :user:`minrk` - Fetch available Julia versions from hosted json :pr:`994` by :user:`tomyun` - Define an interface for Container engines :pr:`848` by :user:`manics` API changes ----------- Bug fixes --------- - Workaround docker-py dependency's failure to import six :pr:`1066:` by :user:`consideratio` - fix: add chardet, a not explicitly declared dependency :pr:`1064` by :user:`johnhoman` - Add build-base to build stage of docker image :pr:`1051` by :user:`yuvipanda` - Fix regression in hydroshare introduced after moving to requests :pr:`1034` by :user:`MridulS` Other merged PRs ---------------- - Update README quay.io URL, Add docker latest tag :pr:`1075` by :user:`manics` - GitHub workflow build and push to Docker hub :pr:`1071` by :user:`manics` - Rename master branch to main :pr:`1068` by :user:`manics` - Remove Pipfile & Pipfile.lock :pr:`1054` by :user:`yuvipanda` - Remove CircleCI docs build :pr:`1053` by :user:`yuvipanda` - Pin doc requirements to avoid CI breakages :pr:`1052` by :user:`manics` - Stop using deprecated add_stylesheet in sphinx :pr:`1050` by :user:`yuvipanda` - Add study participation notice to readme :pr:`1046` by :user:`sgibson91` - Bump urllib3 from 1.26.4 to 1.26.5 :pr:`1045` by :user:`dependabot` - State newly used installation command :pr:`1040` by :user:`fkohrt` - Bump pyyaml from 5.1.1 to 5.4 :pr:`1029` by :user:`dependabot` - Set default Julia version to 1.6 :pr:`1028` by :user:`tomyun` - Fix logo URL in README :pr:`1027` by :user:`betatim` Version 2021.03.0 ================= `Full changelog `__ New features ------------ - freeze with mamba, add 3.9 :pr:`1017` by :user:`minrk` - Add GH workflow to push releases to PYPi and introduce CalVer :pr:`1004` by :user:`betatim` - Add entrypoint script which automatically propagates \*_PROXY env vars… :pr:`1003` ([@g-braeunlich](https://github.com/g-braeunlich)) - Update to JupyterLab 3.0 :pr:`996` by :user:`jtpio` - Fetch available Julia versions from hosted json :pr:`994` by :user:`tomyun` - Add a contentprovider for Software Heritage persistent ID (SWHID) :pr:`988` by :user:`douardda` - Stream jupyter server logs to a file :pr:`987` by :user:`betatim` - add 4.0, 4.0.2 to list of supported R versions :pr:`960` by :user:`minrk` API changes ----------- Bug fixes --------- - fix dataverse regression introduced in last release :pr:`1011` by :user:`MridulS` - buildpacks.r: dont use apt-key directly to respect \*_proxy env vars :pr:`1019` ([@g-braeunlich](https://github.com/g-braeunlich)) Other merged PRs ---------------- - Cleanup install_requires including duplicates :pr:`1020` by :user:`manics` - bump docker action version :pr:`1018` by :user:`minrk` - bump python in circleci test :pr:`1013` by :user:`minrk` - Investigating the missing logs :pr:`1008` by :user:`betatim` - Experiment with different install mechanism to get code coverage stats again :pr:`982` by :user:`betatim` Version 2021.01.0 ================= `Full changelog `__ New features ------------ - Replace urllib by requests in contentproviders :pr:`993` by :user:`douardda` - Use mambaforge instead of miniforge :pr:`992` by :user:`SylvainCorlay` - buildpacks/nix: 2.3 -> 2.3.9 :pr:`991` by :user:`FRidh` - Drop support for stencila :pr:`985` by :user:`minrk` - Add Julia 1.5.3 support :pr:`984` by :user:`tomyun` - Update to node 14 :pr:`983` by :user:`jtpio` - Mamba 0.6.1 :pr:`979` by :user:`minrk` - Ensure REPO_DIR owned by NB_USER :pr:`975` by :user:`tomyun` - Add Julia 1.5.2 support :pr:`965` by :user:`tomyun` - Mamba number three :pr:`962` by :user:`SylvainCorlay` - Add a Mercurial contentprovider :pr:`950` by :user:`paugier` - Add Julia 1.5.1 support :pr:`949` by :user:`tomyun` - Handle requirements.txt with `--pre` lines :pr:`943` by :user:`betatim` - Add Julia 1.5.0 support :pr:`938` by :user:`tomyun` - Update JupyterLab to 2.2.0 :pr:`933` by :user:`manics` - Bump nix version to 2.3 :pr:`915` by :user:`jboynyc` - Add nbresuse==0.3.3 (full freeze.py) :pr:`904` by :user:`manics` - Add Julia 1.4.2 support :pr:`899` by :user:`davidanthoff` - Bump version of irkernel for R 4.0 :pr:`892` by :user:`betatim` - chmod start script from repo2docker-entrypoint :pr:`886` by :user:`danlester` - pypi jupyter-offlinenotebook==0.1.0 :pr:`880` by :user:`manics` - Add support for Julia 1.4.1 :pr:`878` by :user:`davidanthoff` - Change --env option to work like docker's :pr:`874` by :user:`hwine` - Add support for Julia 1.4.0 :pr:`870` by :user:`davidanthoff` - Update server proxy and rsession proxy :pr:`869` by :user:`betatim` - Use miniforge instead of miniconda to get conda :pr:`859` by :user:`yuvipanda` - If looking for latest MRAN URL try earlier snapshots too :pr:`851` by :user:`manics` - Add jupyter-offlinenotebook extension :pr:`845` by :user:`betatim` API changes ----------- - Bump Python requirement to 3.6 from 3.5 :pr:`951` by :user:`betatim` Bug fixes --------- - buildpacks/nix: disable sandboxing (bugfix) :pr:`990` by :user:`FRidh` - avoid deprecated import of collections.abc :pr:`924` by :user:`minrk` - Add missing “:” for R code :pr:`900` by :user:`adamhsparks` - Fix RShiny proxy :pr:`893` by :user:`betatim` - Work around a Julia bug :pr:`879` by :user:`davidanthoff` - Fix typo :pr:`862` by :user:`jtpio` Other merged PRs ---------------- - Fix figshare test :pr:`1001` by :user:`manics` - Weekly test of master to check for external failures :pr:`998` by :user:`manics` - Remove reference to `master` branch from CLI doc :pr:`977` by :user:`betatim` - add chown to COPY commands to reduce layer count :pr:`969` by :user:`bollwyvl` - set TIMEFORMAT for timed bash conda commands :pr:`966` by :user:`manics` - Disable jupyterlab extension build minimize :pr:`963` by :user:`manics` - Bump Black version to 20.8b1 and use --target-version=py36 :pr:`955` by :user:`paugier` - Add workflow to build Docker image :pr:`954` by :user:`manics` - Crosslink 'Configuring your repository' with usage :pr:`952` by :user:`manics` - Add `www-frame-origin=same` to /etc/rstudio/rserver.conf :pr:`944` ([@rkevin-arch](https://github.com/rkevin-arch)) - GitHub Actions :pr:`942` by :user:`minrk` - stop running tests on travis :pr:`940` by :user:`minrk` - update repo URLs for jupyterhub/repo2docker :pr:`939` by :user:`minrk` - Upgrade custom test infrastructure for pytest 6.0.0 :pr:`936` by :user:`betatim` - validate_image_name: mention lowercase, fix formatting :pr:`934` by :user:`manics` - Update snapshot date for simple R test :pr:`930` by :user:`betatim` - little improvement for testing binder_dir :pr:`928` by :user:`bitnik` - update docs for config dirs :pr:`927` by :user:`bitnik` - doc: runtime.txt installs python x.y (& concise rewording) :pr:`914` by :user:`mdeff` - doc: environment.yml installs a conda env, not only python :pr:`913` by :user:`mdeff` - Make the memory limit test simpler :pr:`912` by :user:`betatim` - Add gitpod.io config for docs :pr:`908` by :user:`betatim` - fix repo2docker logo in Sphinx docs :pr:`906` by :user:`trallard` - Update Dockerfile to add Docker :pr:`896` by :user:`hamelsmu` - Document test failure workarounds :pr:`890` by :user:`hwine` - Workaround Docker issue impacting some tests on macOS :pr:`882` by :user:`hwine` - [docs] fix grammatical error in section title :pr:`872` by :user:`jameslamb` - Fix long form args requirements :pr:`866` by :user:`betatim` - Adopt new Sphinx theme name :pr:`864` by :user:`xhochy` - Document loose conda export with --from-history :pr:`863` by :user:`xhochy` - utils.execute_cmd flush buffer if no EOL :pr:`850` by :user:`manics` - Update black 19.10b0, target Python 3.5 :pr:`849` by :user:`manics` - docs: postBuild warn about shell script errors being ignored :pr:`844` by :user:`manics` - Update changelog for 0.11.0 :pr:`842` by :user:`betatim` Version 0.11.0 ============== Release date: 2020-02-05 New features ------------ - Add support for Figshare in :pr:`788` by :user:`nuest`. - Add support for Dataverse in :pr:`739` by :user:`Xarthisius`. - Add support for configuring the version of R installed in :pr:`772` by :user:`betatim`. - Add support for Julia 1.2.0 in :pr:`768` by :user:`davidanthoff`. - Add support for Julia 1.3.0 and 1.0.5 in :pr:`822` by :user:`davidanthoff`. - Add support for Julia 1.3.1 in :pr:`831` by :user:`davidanthoff`. - Update Miniconda to 4.7.10 in :pr:`769` by :user:`davidrpugh`. - Update IRKernel to 1.0.2 in :pr:`770` by :user:`GeorgianaElena`. - Update RStudio to 1.2 in :pr:`803` by :user:`pablobernabeu`. - Switch to "pandas" sphinx theme for documentation in :pr:`816` by :user:`choldgraf`. - Add content provider documentation in :pr:`824` by :user:`choldgraf`. - Remove legacy buildpack in :pr:`829` by :user:`betatim`. - Add support for automatic RStudio install when using R packages via conda in :pr:`838` by :user:`xhochy`. - Add support for Python 3.8 in :pr:`840` by :user:`minrk`. - Add Hydroshare as content provider in :pr:`800` by :user:`sblack-usu`. - Update to Jupyter Notebook 6 and Lab 1.2 in :pr:`839` by :user:`minrk`. Bug fixes --------- - Fix for submodule check out in :pr:`809` by :user:`davidbrochart`. - Handle `requirements.txt` files with different encodings in :pr:`771` by :user:`GeorgianaElena`. - Update to nteract-on-jupyter 2.1.3 in :pr:`2.1.3 by :user:`betatim`. - Use `useradd --no-log-init` to fix exhausting disk space in :pr:`804` by :user:`manics.` - Add help text for commandline arguments in :pr:`517` by :user:`yuvipanda`. - Fix submodule checkout in :pr:`809` by :user:`davidbrochart`. Version 0.10.0 ============== Release date: 2019-08-07 New features ------------ - Increased minimum Python version supported for running `repo2docker` itself to Python 3.5 in :pr:`684` by :user:`betatim`. - Support for `Pipfile` and `Pipfile.lock` implemented in :pr:`649` by :user:`consideratio`. - Use only conda packages for our base environments in :pr:`728` by :user:`scottyhq`. - Fast rebuilds when repo dependencies haven't changed by :user:`minrk` and :user:`betatim` in :pr:`743`, :pr:`752`, :pr:`718` and :pr:`716`. - Add support for Zenodo in :pr:`693` by :user:`betatim`. - Add support for general Invenio repositories in :pr:`704` by :user:`tmorrell`. - Add support for julia 1.0.4 and 1.1.1 in :pr:`710` by :user:`davidanthoff`. - Bump Conda from 4.6.14 to 4.7.5 in :pr:`719` by :user:`davidrpugh`. API changes ----------- Bug fixes --------- - Prevent building the image as root if --user-id and --user-name are not specified in :pr:`676` by :user:`Xarthisius`. - Add bash to Dockerfile to fix usage of private repos with git-crendential-env in :pr:`738` by :user:`eexwhyzee`. - Fix memory limit enforcement in :pr:`677` by :user:`betatim`. Version 0.9.0 ============= Release date: 2019-05-05 New features ------------ - Support for julia `Project.toml`, `JuliaProject.toml` and `Manifest.toml` files in :pr:`595` by :user:`davidanthoff` - Set JULIA_PROJECT globally, so that every julia instance starts with the julia environment activated in :pr:`612` by :user:`davidanthoff`. - Update Miniconda version to 4.6.14 and Conda version to 4.6.14 in :pr:`637` by :user:`jhamman` - Install notebook into `notebook` env instead of `root`. Activate conda environments and shell integration via ENTRYPOINT in :pr:`651` by :user:`minrk` - Support for `.binder` directory in addition to `binder` directory for location of configuration files, in :pr:`653` by :user:`jhamman`. - Updated contributor guide and issue templates for bugs, feature requests, and support questions in :pr:`654` and :pr:`655` by :user:`KirstieJane` and :user:`betatim`. - Create a page naming and describing the "Reproducible Execution Environment Specification" (the specification used by repo2docker) in :pr:`662` by :user:`choldgraf`. API changes ----------- Bug fixes --------- - Install IJulia kernel into ${NB_PYTHON_PREFIX}/share/jupyter in :pr:`622` by :user:`davidanthoff`. - Ensure git submodules are updated and initilized correctly in :pr:`639` by :user:`djhoese`. - Use archive.debian.org as source for the debian jessie based legacy buildpack in :pr:`633` by :user:`betatim`. - Update to version 5.7.6 of the `notebook` package used in all environments in :pr:`628` by :user:`betatim`. - Update to version 5.7.8 of the `notebook` package and version 2.0.12 of `nteract-on-jupyter` in :pr:`650` by :user:`betatim`. - Switch to newer version of jupyter-server-proxy to fix websocket handling in :pr:`646` by :user:`betatim`. - Update to pip version 19.0.3 in :pr:`647` by :user:`betatim`. - Ensure ENTRYPOINT is an absolute path in :pr:`657` by :user:`yuvipanda`. - Fix handling of `--build-memory-limit` values without a postfix in :pr:`652` by :user:`betatim`. Version 0.8.0 ============= Release date: 2019-02-21 New features ------------ - Add additional metadata to docker images about how they were built :pr:`500` by :user:`jrbourbeau`. - Allow users to install global NPM packages: :pr:`573` by :user:`GladysNalvarte`. - Add documentation on switching the user interface presented by a container. :pr:`568` by user:`choldgraf`. - Increased test coverage to ~87% by :user:`betatim` and :user:`yuvipanda`. - Documentation improvements and additions by :user:`lheagy`, :user:`choldgraf`. - Remove f-strings from code base, repo2docker is compatible with Python 3.4+ again by :user:`jrbourbeau` in :pr:`520`. - Local caching of previously built repostories to speed up launch times by :user:`betatim` in :pr:`511`. - Make destination of repository content in the container image configurable on the CLI via ``--target-repo-dir``. By :user:`yuvipanda` in :pr:`507`. - Expose CPU limit settings for building and running containers. By :user:`GladysNalvarte` in :pr:`579`. - Make Python 3.7 the default version. By :user:`yuvipanda` and :user:`minrk` in :pr:`539`. API changes ----------- Bug fixes --------- - In some cases the version of conda installed in images was not pinned and got upgraded by user actions. Fixed in :pr:`576` by :user:`minrk`. - Fix an error related to checking if debug output was enabled or not: :pr:`575` by :user:`yuvipanda`. - Update nteract frontend to version 2.0.0 by :user:`yuvipanda` in :pr:`571`. - Fix quoting issue in ``GIT_CREDENTIAL_ENV`` environment variable by :user:`minrk` in :pr:`572`. - Change to using the first 8 characters of each Git commit, not the last 8, to tag each built docker image of repo2docker itself. :user:`minrk` in :pr:`562`. - Allow users to select the Julia when using a ``requirements.txt`` by :user:`yuvipanda` in :pr:`557`. - Set ``JULIA_DEPOT_PATH`` to install packages outside the home directory by :user:`yuvipanda` in :pr:`555`. - Update to Jupyter notebook 5.7.4 :pr:`519` by :user:`minrk`. Version 0.7.0 ============= Release date: 2018-12-12 New features ------------ - Build from sub-directory: build the image based on a sub-directory of a repository :pr:`413` by :user:`dsludwig`. - Editable mode: allows editing a local repository from a live container :pr:`421` by :user:`evertrol`. - Change log added :pr:`426` by :user:`evertrol`. - Documentation: improved the documentation for contributors :pr:`453` by :user:`choldgraf`. - Buildpack: added support for the nix package manager :pr:`407` by :user:`costrouc`. - Log a 'success' message when push is complete :pr:`482` by :user:`yuvipanda`. - Allow specifying images to reuse cache from :pr:`478` by :user:`yuvipanda`. - Add JupyterHub back to base environment :pr:`476` by :user:`yuvipanda`. - Repo2docker has a logo! by :user:`agahkarakuzu` and :user:`blairhudson`. - Improve support for Stencila, including identifying stencila runtime from document context :pr:`457` by :user:`nuest`. API changes ----------- - Add content provider abstraction :pr:`421` by :user:`betatim`. Bug fixes --------- - Update to Jupyter notebook 5.7 :pr:`475` by :user:`betatim` and :user:`minrk`. Version 0.6 =========== Released 2018-09-09 Version 0.5 =========== Released 2018-02-07 Version 0.4.1 ============= Released 2018-09-06 Version 0.2 =========== Released 2018-05-25 Version 0.1.1 ============= Released 2017-04-19 Version 0.1 =========== Released 2017-04-14