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[GRDM-63906] Upstreamの取り込み (2026.04.0) - #31

Merged

ikfj merged 395 commits into

RCOSDP:masterfrom

yacchin1205:feature/upstream-2026.04.0

Oct 30, 2026

Merged

[GRDM-63906] Upstreamの取り込み (2026.04.0)#31
ikfj merged 395 commits into
RCOSDP:masterfrom
yacchin1205:feature/upstream-2026.04.0

This pull request is big! We're only showing the most recent 250 commits

Commits on Jul 9, 2025
- Add --vanilla to R call
  rgaiacs
  committed
  bcb46e1
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  356371d
Commits on Aug 1, 2025
- Revamp our documentation and refactor a bit (#1433)
  
  choldgraf
  and
  pre-commit-ci[bot]
  authored
  6cf91e4
Commits on Aug 3, 2025
- Simplify our release docs
  choldgraf
  committed
  714d4e3
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  0b12f5f
Commits on Aug 8, 2025
- Add note on root
  choldgraf
  committed
  b5e4b3c
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  b190934
Commits on Aug 14, 2025
- Avoid use of jupyter-repo2docker
  rgaiacs
  committed
  ab26c12
- Add a admonition regading the name of the package on PyPI
  rgaiacs
  committed
  2c25648
- Review "User guide" index page
  rgaiacs
  committed
  1a67731
- Merge pull request #1432 from rgaiacs/1431-vanilla
  manics
  authored
  3899104
- Merge pull request #1438 from rgaiacs/1437-avoid-jupyter-repo2docker
  yuvipanda
  authored
  1f1fab0
Commits on Aug 15, 2025
- Review "Four ways to use repo2docker images" page
  rgaiacs
  committed
  564eb0d
- Review "Configuration files supported by repo2docker" page
  rgaiacs
  committed
  e3d3e2b
- Review "Configuration files supported" page
  rgaiacs
  committed
  ba71070
- Fix list of supported R versions in the documentation
  rgaiacs
  committed
  8b3f8cc
Commits on Aug 16, 2025
- Merge pull request #1394 from jupyterhub/pre-commit-ci-update-config
  yuvipanda
  authored
  a55f54b
- Merge pull request #1434 from choldgraf/release-docs
  yuvipanda
  authored
  ac4f14d
Commits on Aug 18, 2025
- Improve documentation index page
  rgaiacs
  committed
  765757e
- Merge pull request #1442 from rgaiacs/improve-documentation
  manics
  authored
  09b056e
- Upgrade R to 4.4.2
  rgaiacs
  committed
  6cb5210
- Fix test for default version of R
  rgaiacs
  committed
  80e561a
- Fix more test related with R version
  rgaiacs
  committed
  d83fd10
- Change the date used for the R snapshot
  rgaiacs
  committed
  f2641f3
Commits on Aug 19, 2025
- Add some missing words
  yuvipanda
  authored
  387155a
- Merge pull request #1436 from choldgraf/root
  yuvipanda
  authored
  5870d2b
- Merge pull request #1401 from rgaiacs/1384-upgrade-r
  yuvipanda
  authored
  734a729
- Merge pull request #1445 from rgaiacs/review-index-page
  yuvipanda
  authored
  2552e01
Commits on Aug 21, 2025
- Replace --vanilla with --no-init-file
  rgaiacs
  committed
  673e1bd
- Merge pull request #1451 from rgaiacs/1450-fix-vanilla
  rgaiacs
  authored
  724ac17
Commits on Aug 22, 2025
- Fail earlier when user try to install future version of R
  rgaiacs
  committed
  88d489d
- Add check for docker buildx
  rgaiacs
  committed
  9bf010e
- Merge pull request #1457 from rgaiacs/1452-check-buildx
  yuvipanda
  authored
  ab2fe4e
Commits on Aug 23, 2025
- 从setup迁移至toml
  lixiname
  committed
  ffaa9bb
Commits on Aug 25, 2025
- 完成了从setup->toml的迁移
   lixiname
  committed
  fe7bce0
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  a78d344
- add support for R 4.5.1
  shaneknapp
  committed
  13134ce
Commits on Aug 26, 2025
- porting tests to r4.5.1
  shaneknapp
  committed
  e588293
- fat-fingered month from the cran repo: https://cran.r-project.org/src/base/R-4/
  shaneknapp
  committed
  541229b
- Merge pull request #1460 from shaneknapp/add-r-451
  yuvipanda
  authored
  7292f54
Commits on Aug 27, 2025
- s/contributing/contribute/g
  shaneknapp
  committed
  48cf039
Commits on Aug 28, 2025
- Merge pull request #1461 from shaneknapp/fix-broken-contrib-roadmap-link
  rgaiacs
  authored
  f2de11f
- Support R full version provided by user
  rgaiacs
  committed
  3079a04
- Add missing 2025.08.0 release in changelog
  
  choldgraf
  authored and
  rgaiacs
  committed
  2a14312
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  4215484
- Merge pull request #1428 from manics/runtime-version-date
  manics
  authored
  664c272
- Merge branch 'main' into 1449-add-missing-changelog
  manics
  authored
  00df77b
- Merge pull request #1462 from rgaiacs/1449-add-missing-changelog
  manics
  authored
  32503ab
Commits on Sep 1, 2025
- Always call `ContainerEngine.build()` when `push`ing
  manics
  committed
  bc5704d
Commits on Sep 3, 2025
- Bump mamba from 2.1.0 to 2.3.2
  weiji14
  committed
  c054a36
- Merge pull request #1464 from manics/push-always-build
  manics
  authored
  1766748
- Merge branch 'main' into 1455-fail-earlier
  minrk
  authored
  53e8ce1
- Switch downgrade check to be on krb5=1.17.2 that pins to openssl=1.1.1
  weiji14
  committed
  0e47641
- Bump conda from 24.11.0 to 25.7.0
  weiji14
  committed
  f5c8366
Commits on Sep 7, 2025
- Merge branch 'main' into mamba/2.3.2
  weiji14
  committed
  38478f8
Commits on Sep 8, 2025
- Address comments from @minrk
  rgaiacs
  committed
  1f83d76
- Remove requirement of date in runtime.txt for R
  rgaiacs
  committed
  460d3c1
- Replace warning with info in log
  rgaiacs
  committed
  6b00d6f
- Minor improvement on English in error message
  rgaiacs
  committed
  b650d28
Commits on Sep 16, 2025
- Fix broken readme doc links
  agitter
  authored
  ff6fb61
- Merge pull request #1466 from agitter/patch-1
  minrk
  authored
  314f64b
Commits on Oct 1, 2025
- Bump actions/checkout from 4 to 5
  dependabot[bot]
  authored
  6e1865f
- Merge pull request #1469 from jupyterhub/dependabot/github_actions/actions/checkout-5
  consideRatio
  authored
  9fc72e2
- Bump actions/setup-python from 5 to 6
  dependabot[bot]
  authored
  9f49f74
- Merge pull request #1470 from jupyterhub/dependabot/github_actions/actions/setup-python-6
  consideRatio
  authored
  703a864
- Add Python 3.13 to freeze.py
  rgaiacs
  committed
  dfa405b
- Update conda environments
  rgaiacs
  committed
  1269dd2
- fix venv/postBuild test
  minrk
  committed
  a39849b
- Merge pull request #1456 from rgaiacs/1455-fail-earlier
  minrk
  authored
  25c9c30
Commits on Oct 2, 2025
- Merge pull request #1447 from rgaiacs/1446-python-3-13
  rgaiacs
  authored
  882e34c
- Delete gitpod config
  manics
  authored
  690ede8
- Merge pull request #1472 from manics/rm-gitpod
  minrk
  authored
  358888c
Commits on Oct 6, 2025
- [pre-commit.ci] pre-commit autoupdate
  pre-commit-ci[bot]
  authored
  430d707
Commits on Oct 10, 2025
- Merge pull request #1473 from jupyterhub/pre-commit-ci-update-config
  minrk
  authored
  323fa90
Commits on Oct 15, 2025
- Add Python 3.14 to list of available versions
  rgaiacs
  committed
  5406885
- fix import of datetime.timezone.utc
  minrk
  committed
  45c24d1
- Merge pull request #1406 from yuvipanda/utcnow-warning
  minrk
  authored
  0f3dd3c
- Merge branch 'main' into mamba/2.3.2
  yuvipanda
  authored
  8936600
- Bump conda from 25.7.0 to 25.9.1
  weiji14
  committed
  8f6c01c
Commits on Oct 16, 2025
- Updating conda buildpacks for Python <= 3.12
  rgaiacs
  committed
  69279c5
- Updating conda buildpacks for Python == 3.13
  rgaiacs
  committed
  638911c
- Add conda buildpacks for Python == 3.14
  rgaiacs
  committed
  9b85b72
- Merge pull request #1476 from rgaiacs/1446-missing-files
  rgaiacs
  authored
  6e88d98
- Merge pull request #1475 from rgaiacs/1474-python-3-14
  minrk
  authored
  067e14a
Commits on Oct 20, 2025
- Bump base image used to latest LTS
  
  yuvipanda
  authored and
  minrk
  committed
  df7ff49
- update docs with 24.04
  minrk
  committed
  1fafb95
Commits on Oct 22, 2025
- fetch dataverse installations at runtime
  minrk
  committed
  fe215ba
- finish updating to pyproject.toml
  minrk
  committed
  a6e02db
- only install repo2docker itself
  minrk
  committed
  0fad1b6
- invoke setuptools_scm to get version
  minrk
  committed
  6879944
- Merge branch 'main' into main
  minrk
  authored
  12df2be
- invoke setuptools_scm to get version
  minrk
  committed
  0024f21
- Merge pull request #1479 from minrk/dataverse-fetch
  manics
  authored
  2456a4d
- address review
  minrk
  committed
  f82d077
- Merge pull request #1458 from lixiname/main
  minrk
  authored
  6d46061
- require Python 3.10
  minrk
  committed
  850c1d9
Commits on Oct 23, 2025
- update prettier pre-commit mirror
  minrk
  committed
  924a54a
Commits on Oct 27, 2025
- Merge pull request #1481 from minrk/require-310
  minrk
  authored
  24211ec
Commits on Oct 28, 2025
- mamba 2.3.3
  minrk
  committed
  91ce094
- restore downgrade/verify test
  minrk
  committed
  fb72937
Commits on Oct 29, 2025
- Merge pull request #1465 from weiji14/mamba/2.3.2
  minrk
  authored
  978fefc
Commits on Nov 1, 2025
- Bump actions/upload-artifact from 4 to 5
  dependabot[bot]
  authored
  8a0b11b
- Merge pull request #1482 from jupyterhub/dependabot/github_actions/actions/upload-artifact-5
  manics
  authored
  4992a43
Commits on Nov 3, 2025
- [pre-commit.ci] pre-commit autoupdate
  pre-commit-ci[bot]
  authored
  e855800
Commits on Nov 4, 2025
- Add item to FAQ regarding rootless mode
  rgaiacs
  committed
  f87ca4b
- Merge pull request #1485 from rgaiacs/1483-doc-rootless
  manics
  authored
  53e6f77
- Merge pull request #1484 from jupyterhub/pre-commit-ci-update-config
  minrk
  authored
  443b851
Commits on Nov 13, 2025
- Start implementation of support for pyproject.yml
  rgaiacs
  committed
  4f9b799
- Add builldpack for pyproject to list of buildpack
  rgaiacs
  committed
  1ad4737
- Avoid change PATH during bash command
  rgaiacs
  committed
  9e5b8d9
- Change Python version used by ReadTheDocks
  rgaiacs
  committed
  411938c
- Reduce code duplication in PyprojectBuildPack
  rgaiacs
  committed
  bb1b6d3
- Use tomli for Python < 3.11
  rgaiacs
  committed
  fd67aff
- Check that pyproject.toml has required fields
  rgaiacs
  committed
  0e74169
- Add one test for pyproject
  rgaiacs
  committed
  d1175b6
- Add documentation about pyproject.toml
  rgaiacs
  committed
  16f0884
- Fix English typos
  rgaiacs
  committed
  e3e7e4c
- Only read pyproject.toml if file exists
  rgaiacs
  committed
  0cb7093
- Merge PyprojectBuildPack into PythonBuildPack
  rgaiacs
  committed
  f9ff175
- Add packaging as dependence
  rgaiacs
  committed
  3f5029e
- Improve Python version detection in PythonBuildPack
  rgaiacs
  committed
  355c1cd
- Make sure that _python_version always include major and minor
  rgaiacs
  committed
  6183e4f
Commits on Nov 18, 2025
- update hydroshare download urls
  sblack-usu
  committed
  29640d5
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  55a2402
Commits on Nov 19, 2025
- Merge pull request #1488 from sblack-usu/hs-s3-update
  rgaiacs
  authored
  bcbaf38
Commits on Nov 21, 2025
- Improve comments in Python buildpack
  
  rgaiacs
  and
  minrk
  authored
  250ab4c
- Add _is_python_package() to Python build package
  rgaiacs
  committed
  b0d5c9a
Commits on Nov 24, 2025
- Simplify detect() for Python buildpack
  rgaiacs
  committed
  98aa00b
- Simplify _should_preassemble_pip() for Python buildpack
  rgaiacs
  committed
  e1f8747
- Allow Python buildpack to select Python version
  rgaiacs
  committed
  c9a40b4
- Write logs to tmp location if there's no disk left
  GeorgianaElena
  committed
  f1aa356
- Merge pull request #1444 from rgaiacs/1427-support-pyproject
  minrk
  authored
  b9c08f4
Commits on Nov 25, 2025
- Just stop writing the logs if we run out of space
  GeorgianaElena
  committed
  835e613
- Rename, add docstrings and close file
  GeorgianaElena
  committed
  1a571bd
Commits on Dec 1, 2025
Commits on Dec 2, 2025
- Merge pull request #1491 from jupyterhub/pre-commit-ci-update-config
  minrk
  authored
  d850c15
Commits on Dec 3, 2025
- Merge pull request #1489 from GeorgianaElena/handle-no-space
  minrk
  authored
  e792c9b
Commits on Dec 4, 2025
- Update link for creating a release
  GeorgianaElena
  authored
  b2c5fb8
Commits on Dec 8, 2025
- BUG: COPY --chmod=0755 /usr/local/bin/{python3-login,repo2docker-entrypoint} to support rootless podman
  
  westurner
  authored and
  minrk
  committed
  9b287fb
- Merge pull request #1395 from westurner/patch-3
  minrk
  authored
  9c50d4d
- Merge pull request #1492 from jupyterhub/update-release-link
  minrk
  authored
  b796c5a
- add redirects for PR 1433
  minrk
  committed
  345a890
- Fix lint warnings in simple test Dockerfile
  DAKSH-coder26
  committed
  039df2b
Commits on Dec 9, 2025
- New release
  GeorgianaElena
  committed
  f54386b
- Update the release process
  GeorgianaElena
  committed
  091a75e
- Merge pull request #1494 from DAKSH-coder26/fix-jsonargsrecommended-1477
  minrk
  authored
  2844080
- Merge pull request #1493 from minrk/rediraffe-contributing
  minrk
  authored
  ec3b487
Commits on Dec 10, 2025
- Fix version number
  
  GeorgianaElena
  and
  minrk
  authored
  54fff4f
- Merge pull request #1495 from GeorgianaElena/new-release
  GeorgianaElena
  authored
  ee66d9c
- Mark the PR as a breaking change
  GeorgianaElena
  committed
  b896b00
- Merge pull request #1496 from GeorgianaElena/breaking-change
  GeorgianaElena
  authored
  352fd2f
Commits on Jan 1, 2026
- Bump actions/upload-artifact from 5 to 6
  dependabot[bot]
  authored
  2ad4823
Commits on Jan 4, 2026
- Merge pull request #1497 from jupyterhub/dependabot/github_actions/actions/upload-artifact-6
  manics
  authored
  be1e551
Commits on Jan 5, 2026
- Fix typo in pyproject.toml file name
  rgaiacs
  committed
  48969c2
- Merge pull request #1499 from rgaiacs/1498-typo-file
  rgaiacs
  authored
  c8b2679
- [pre-commit.ci] pre-commit autoupdate
  pre-commit-ci[bot]
  authored
  fb599ce
Commits on Jan 8, 2026
- Merge pull request #1500 from jupyterhub/pre-commit-ci-update-config
  rgaiacs
  authored
  ca21e1b
- Add support to DockerEngine
  rgaiacs
  committed
  4ae4be0
- Use "container" instead of Docker when possible in index.md
  rgaiacs
  committed
  3108885
- Use "container" instead of Docker when possible in start.md
  rgaiacs
  committed
  45c3fb3
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  
  pre-commit-ci[bot]
  authored and
  rgaiacs
  committed
  5f17fed
- Auto configure container_cli property based on DOCKER_HOST
  rgaiacs
  committed
  606cc87
- Add podman as container cli for GitHub Actions
  rgaiacs
  committed
  d4fc92d
- Select correct hostname for Podman
  rgaiacs
  committed
  d1985fb
- Add note about Podman service to documentation
  rgaiacs
  committed
  905fe0b
- Enable Podman socket during test
  rgaiacs
  committed
  080f61b
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  
  pre-commit-ci[bot]
  authored and
  rgaiacs
  committed
  916d3c1
- Avoid infinite loop in test
  rgaiacs
  committed
  b0ad00b
- Hide output of "docker version" test
  rgaiacs
  committed
  f05f420
- Add WorkingDir to bridge the gap with Podman
  rgaiacs
  committed
  8d74803
- Fix tests/unit/test_app.py::test_extra_buildx_build_args
  rgaiacs
  committed
  7ac468a
- Make DOCKER_HOST more robust
  rgaiacs
  committed
  3027e2c
- Prefer to use attribute over internal variable
  rgaiacs
  committed
  e1807c5
- Minor improve to docker.py wrap
  rgaiacs
  committed
  07808e6
- Expose DOCKER_CLI from docker.py
  rgaiacs
  committed
  f29e7de
- Mark some tests with @pytest.mark.skipif
  rgaiacs
  committed
  f73d267
- Skip registry test for Podman
  rgaiacs
  committed
  ba52252
- Fix English mistakes in documentation
  rgaiacs
  committed
  7063a1f
- Reduce the number of tests for Podman
  rgaiacs
  committed
  308ac22
- Add comment explaining DOCKER_HOST
  rgaiacs
  committed
  37d2612
- Guard subprocess.run() with try block
  
  rgaiacs
  and
  minrk
  committed
  fee0b11
- Re-write matrix strategy to use include
  rgaiacs
  committed
  9259ca8
- Remove if-block already cover in try-block
  rgaiacs
  committed
  7270129
- Fix include for GItHub Actions
  rgaiacs
  committed
  7f6b65e
Commits on Jan 13, 2026
- Delete container and image after test
  rgaiacs
  committed
  6baaf08
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  f010e36
Commits on Jan 14, 2026
- Disable test of conda for podman
  rgaiacs
  committed
  9032292
- Handle existing NB_UID/NB_GID
  
  manics
  authored and
  minrk
  committed
  2d78af2
- add test for uid=1000 clobbering
  minrk
  committed
  b1243fc
- update date for 24.04
  minrk
  committed
  033b861
- fix base permission test
  minrk
  committed
  8f5aef5
Commits on Jan 15, 2026
- update date in one more place
  minrk
  committed
  91d6ab5
Commits on Jan 20, 2026
- Add support to both .yml and .yaml
  rgaiacs
  committed
  c62e250
- Add self.environment_yaml_path to Conda buildpack
  rgaiacs
  committed
  bbd38c8
- Fix rename from self.environment_yml to self.environment_yaml_path
  rgaiacs
  committed
  d727bd7
Commits on Jan 21, 2026
- Merge pull request #1471 from rgaiacs/document-podman-support
  rgaiacs
  authored
  8ff237f
- Fix logic in environment_yaml_path()
  rgaiacs
  committed
  1f80471
Commits on Jan 22, 2026
- Fix typo
  rgaiacs
  committed
  0ef03d4
Commits on Jan 23, 2026
- Merge pull request #1501 from rgaiacs/1373-yaml
  minrk
  authored
  97eda49
- Merge pull request #1417 from yuvipanda/ubuntu-update
  minrk
  authored
  a0a7fec
Commits on Mar 1, 2026
- Bump actions/upload-artifact from 6 to 7
  dependabot[bot]
  authored
  1b45e59
Commits on Mar 2, 2026
Commits on Mar 6, 2026
- Merge pull request #1502 from jupyterhub/pre-commit-ci-update-config
  minrk
  authored
  500d3c9
- Clarify where/how repo2docker locates config files
  chuckwondo
  committed
  7368b7e
Commits on Mar 9, 2026
- Merge pull request #1509 from chuckwondo/main
  rgaiacs
  authored
  1fdc85f
- pin chardet < 7
  minrk
  committed
  b83446f
- fix import of universaldetector
  minrk
  committed
  3f4296f
- actually, let's avoid chardet altogether
  minrk
  committed
  847980b
- Merge pull request #1510 from minrk/pin-chardet
  minrk
  authored
  25198d8
- freeze requirements in Dockerfile
  minrk
  committed
  2b6121a
- allow default_buildpack=None to disable building when no env is detected
  minrk
  committed
  7db6108
Commits on Mar 10, 2026
- add refreeze
  minrk
  committed
  89d0fb8
Commits on Mar 13, 2026
- Merge pull request #1511 from minrk/allow-no-default
  manics
  authored
  6b59faf
- add dependencies label to dependabot prs
  
  minrk
  and
  manics
  authored
  1f1d592
Commits on Apr 1, 2026
Commits on Apr 6, 2026
- [pre-commit.ci] pre-commit autoupdate
  pre-commit-ci[bot]
  authored
  7b64330
Commits on Apr 17, 2026
- Merge pull request #1512 from minrk/freeze-docker
  minrk
  authored
  f07b372
- Merge pull request #1519 from jupyterhub/pre-commit-ci-update-config
  minrk
  authored
  cd25cef
- try to fix dependabot for Dockerfile
  minrk
  committed
  a02ea00
- update shiny-proxy to 1.4
  minrk
  committed
  9031649
- fix figshare url regex
  minrk
  committed
  5edd091
- R: install with pak
  minrk
  committed
  066b12c
- clear cache after pak install
  minrk
  committed
  09cadb5
Commits on Apr 18, 2026
- manually cleanup after pak
  minrk
  committed
  37e5fbd
- remotes doesn't leave a mess
  minrk
  committed
  6882be5
- upgrade in refreeze
  minrk
  committed
  aa16a27
Commits on Apr 21, 2026
- Merge pull request #1530 from minrk/install_local
  manics
  authored
  0cc2e55
- Merge pull request #1529 from minrk/fix-figshare
  manics
  authored
  da706f3
Commits on Apr 22, 2026
- future-proof --no-allow-unsafe
  
  minrk
  and
  manics
  authored
  fcb562c
- missing newline in dataverse log
  minrk
  committed
  ca52d12
- Merge pull request #1527 from minrk/dependabot-group
  manics
  authored
  b5b11fa
- Merge pull request #1526 from minrk/retrieving-log
  manics
  authored
  d3893db
Commits on Oct 28, 2026
- Merge tag '2026.04.0' into feature/upstream-2026.04.0
  yacchin1205
  committed
  a94824b
- Freeze dependencies added by CS-repo2docker
  yacchin1205
  committed
  c1dcc2b
- Update frozen dependencies added by CS-repo2docker
  yacchin1205
  committed
  0787933
- Fix dataverse test due to update in record by author
  
  rgaiacs
  authored and
  yacchin1205
  committed
  0500021
- Fix hydroshare test due to update in record by author
  
  rgaiacs
  authored and
  yacchin1205
  committed
  f44b1d8
- Bump certifi
  yacchin1205
  committed
  f196d32
- Support buildpack-deps:24.04 for MATLAB
  yacchin1205
  committed
  1667007

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