Ecosyste.ms: Issues

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GitHub / nextstrain/cli issues and pull requests

#410 - dev: Explicitly point Read The Docs at our Sphinx configuration file

Pull Request - State: closed - Opened by tsibley about 2 months ago - 1 comment

#409 - Error with bioconda-installed nextstrain.cli when attempting `nextstrain login`

Issue - State: closed - Opened by jgallowa07 2 months ago - 5 comments
Labels: bug

#408 - CI tests failing since 28 Nov

Issue - State: closed - Opened by tsibley 2 months ago - 3 comments

#407 - wip! workflows as programs prototyping

Pull Request - State: open - Opened by tsibley 3 months ago - 16 comments

#406 - runner.aws_batch: Gracefully handle errors when fetching logs for completed jobs

Pull Request - State: closed - Opened by tsibley 3 months ago - 1 comment

#405 - Attaching to Batch job that failed to start results in `ResourceNotFoundException`

Issue - State: closed - Opened by joverlee521 3 months ago - 4 comments
Labels: bug

#404 - dev: Update GitHub runners used by CI

Pull Request - State: closed - Opened by tsibley 4 months ago - 1 comment

#403 - docs: Allow BUILDDIR to be set from environment

Pull Request - State: closed - Opened by victorlin 4 months ago

#402 - dev: Silence new complaint from Mypy in CI

Pull Request - State: closed - Opened by tsibley 4 months ago

#401 - Use :option: directive in --directory help text

Pull Request - State: closed - Opened by victorlin 4 months ago

#399 - wip! dev: Don't compile bytecode for aiohappyeyeballs._staggered in PyOxidizer build

Pull Request - State: closed - Opened by tsibley 4 months ago - 1 comment

#397 - CI failing on all build-standalone steps

Issue - State: closed - Opened by tsibley 4 months ago - 2 comments

#396 - runner.conda: Ignore newly failing type check for tarfile.open()

Pull Request - State: closed - Opened by tsibley 5 months ago

#395 - Communicate why an upload action was not allowed

Issue - State: open - Opened by jameshadfield 6 months ago - 1 comment
Labels: enhancement

#394 - Skip verification of JWT's iat claim

Pull Request - State: closed - Opened by jameshadfield 6 months ago - 4 comments

#393 - aws-batch logs delayed

Issue - State: closed - Opened by joverlee521 6 months ago - 1 comment

#392 - Test new CI workflow

Pull Request - State: closed - Opened by genehack 6 months ago

#390 - Anchor regexes and escape potential metachars [#388]

Pull Request - State: closed - Opened by genehack 6 months ago

#389 - Fix broken links [#388]

Pull Request - State: closed - Opened by genehack 6 months ago

#388 - Fix broken links in docs

Issue - State: closed - Opened by genehack 6 months ago
Labels: documentation

#387 - Bump `conda-incubator/setup-miniconda` action to v3

Pull Request - State: closed - Opened by corneliusroemer 7 months ago - 1 comment

#386 - CI: deprecation warning for node 16 use in setup-miniconda v2

Issue - State: closed - Opened by corneliusroemer 7 months ago - 2 comments
Labels: enhancement

#385 - Pyoxidizer currently unmaintained

Issue - State: closed - Opened by corneliusroemer 7 months ago - 3 comments

#384 - dev: Upgrade setup-miniconda action from v2 → v3

Pull Request - State: closed - Opened by tsibley 7 months ago - 3 comments

#383 - Error during `nextstrain build` after `nextstrain update conda`

Issue - State: closed - Opened by victorlin 7 months ago - 2 comments
Labels: bug

#382 - CI on macOS failing due to IQTREE

Issue - State: closed - Opened by tsibley 7 months ago - 11 comments
Labels: bug

#381 - remote download: Names with dots

Pull Request - State: closed - Opened by tsibley 7 months ago

#380 - `nextstrain remote download` produces bad local filenames when periods are in the dataset name

Issue - State: closed - Opened by tsibley 7 months ago - 2 comments
Labels: bug, source: discussion forum

#379 - Use osx-arm64 packages on Apple silicon

Pull Request - State: open - Opened by victorlin 7 months ago

#377 - CI failing: unable to pull `hello-world:latest`

Issue - State: closed - Opened by victorlin 7 months ago - 1 comment

#376 - Remove/replace macos-11 jobs

Pull Request - State: closed - Opened by victorlin 7 months ago - 1 comment

#375 - Scheduled CI hanging on `macos-11` job

Issue - State: closed - Opened by victorlin 7 months ago

#374 - runner.aws_batch: Download .snakemake/metadata/ too

Pull Request - State: closed - Opened by tsibley 8 months ago - 1 comment

#373 - aws-batch: support Snakemake `--report`

Issue - State: closed - Opened by joverlee521 8 months ago - 7 comments
Labels: enhancement

#371 - Update "build directory" terminology in help and docs

Issue - State: open - Opened by tsibley 9 months ago - 1 comment
Labels: documentation

#370 - build: Add `--exclude-from-upload` and `--exclude-from-download` options

Pull Request - State: closed - Opened by tsibley 9 months ago - 4 comments

#369 - Python 3.12

Pull Request - State: closed - Opened by tsibley 9 months ago - 1 comment

#368 - Officially support Python 3.12

Pull Request - State: closed - Opened by corneliusroemer 10 months ago - 1 comment

#367 - Bump micromamba to 1.5.8

Pull Request - State: closed - Opened by corneliusroemer 10 months ago - 1 comment

#365 - runner: Support NEXTSTRAIN_RUNTIME_ENVDIRS as an alternative to --envdir

Pull Request - State: closed - Opened by tsibley 10 months ago - 1 comment

#364 - doc: Update cross-ref to a main docs project page that moved

Pull Request - State: closed - Opened by tsibley 10 months ago

#363 - shell: Command hangs when `--conda` is used and the runtime has not been set up

Issue - State: open - Opened by victorlin 11 months ago - 13 comments
Labels: bug

#362 - dev: Switch to the org-shared sync-rtd-redirects.yaml workflow

Pull Request - State: closed - Opened by tsibley about 1 year ago

#361 - Check if Rosetta 2 is enabled in the Conda and Docker runner checks

Pull Request - State: closed - Opened by tsibley about 1 year ago - 1 comment

#360 - Unable to set up Singularity runtime on Fred Hutch's `rhino`

Issue - State: closed - Opened by victorlin about 1 year ago - 2 comments
Labels: bug

#359 - Show progress during `check-setup`

Issue - State: open - Opened by corneliusroemer about 1 year ago - 1 comment
Labels: enhancement

#358 - standalone-installer-unix: Use new aarch64 builds for macOS

Pull Request - State: closed - Opened by tsibley about 1 year ago

#357 - Standalone builds for macOS aarch64 (aka arm64, Apple Silicon, M1/M2)

Pull Request - State: closed - Opened by tsibley about 1 year ago - 1 comment

#356 - volume: store_volume("X") no longer sets opts.X

Pull Request - State: closed - Opened by tsibley about 1 year ago - 1 comment

#355 - Better support pathogen repositories which place workflows in subdirectories

Pull Request - State: closed - Opened by tsibley about 1 year ago - 1 comment

#353 - Mention Singularity in a few more lists of runtimes that occur in help and docs

Pull Request - State: closed - Opened by tsibley about 1 year ago - 7 comments

#352 - build(deps): bump actions/upload-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 2 comments
Labels: dependencies

#351 - build(deps): bump actions/download-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#350 - build(deps): bump actions/checkout from 2 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#349 - build(deps): bump actions/setup-python from 2 to 5

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#348 - CI: Write installation commands to job summary

Pull Request - State: closed - Opened by victorlin about 1 year ago

#347 - Review feedback: Support other nextstrain.org-like remotes

Pull Request - State: closed - Opened by tsibley about 1 year ago - 1 comment

#346 - devel/create-github-release: Reflow paragraphs in changelog Markdown to single long lines

Pull Request - State: closed - Opened by tsibley about 1 year ago - 1 comment

#345 - Supporting downloading datasets not in manifest

Pull Request - State: closed - Opened by tsibley about 1 year ago

#344 - dev: Appease Pyright 1.1.345's changed type checking of tuple slices

Pull Request - State: closed - Opened by tsibley about 1 year ago

#343 - runner.singularity: Explicitly support Apptainer's `singularity` when checking versions

Pull Request - State: closed - Opened by tsibley about 1 year ago - 1 comment

#342 - Pass AWS credentials from standard file to Docker

Issue - State: open - Opened by huddlej about 1 year ago - 1 comment
Labels: enhancement

#341 - remote: Show more possible reasons for S3 access error

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#340 - Fix failing Pyright test

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#339 - Unhandled exception when renewing login from a different Cognito user pool

Issue - State: open - Opened by victorlin about 1 year ago - 1 comment
Labels: bug

#338 - doc: Simplify Bioconda installation step

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#337 - Extend validity of login refresh tokens to 90 days from 30 days

Issue - State: closed - Opened by corneliusroemer about 1 year ago - 1 comment
Labels: enhancement

#336 - CLI-ception: Some commands do not work in managed runtime shells

Issue - State: open - Opened by victorlin about 1 year ago - 4 comments
Labels: bug

#335 - Address new Pyright error

Pull Request - State: closed - Opened by victorlin about 1 year ago - 1 comment

#334 - Remotes doc

Pull Request - State: open - Opened by tsibley about 1 year ago

#333 - Support other nextstrain.org-like remotes

Pull Request - State: closed - Opened by tsibley about 1 year ago - 7 comments

#332 - Various and sundry

Pull Request - State: closed - Opened by tsibley about 1 year ago - 2 comments

#331 - remote/s3 should instantiate its own MimeTypes instance

Issue - State: open - Opened by joverlee521 about 1 year ago

#330 - remote: Add zstd to encoding types

Pull Request - State: closed - Opened by joverlee521 about 1 year ago - 1 comment

#329 - Singularity/Apptainer Version

Issue - State: closed - Opened by osageorange over 1 year ago - 4 comments
Labels: bug

#328 - Consider UI/UX for AWS Batch runtime without Docker runtime

Issue - State: open - Opened by joverlee521 over 1 year ago - 3 comments

#327 - Explicitly support Python 3.11

Pull Request - State: closed - Opened by victorlin over 1 year ago

#326 - Cast err.response to Response class for Pyright

Pull Request - State: closed - Opened by victorlin over 1 year ago

#325 - Bump minimum Python version to 3.8

Pull Request - State: closed - Opened by victorlin over 1 year ago - 2 comments

#324 - doc: Update command to retrieve NEXTSTRAIN_COGNITO_CLI_CLIENT_ID

Pull Request - State: closed - Opened by victorlin over 1 year ago - 1 comment

#323 - authn: Handle case when a user is not in any group

Pull Request - State: closed - Opened by victorlin over 1 year ago

#322 - dev: Require Mypy <1.6

Pull Request - State: closed - Opened by tsibley over 1 year ago

#321 - standalone-installer-unix: Use ~/.profile when the default shell is sh

Pull Request - State: closed - Opened by tsibley over 1 year ago - 1 comment

#320 - Broken CI due to upstream release; mypy implicated

Issue - State: closed - Opened by tsibley over 1 year ago - 1 comment
Labels: bug

#319 - Invalid `~/.shrc` file named in standalone installer instructions

Issue - State: closed - Opened by tsibley over 1 year ago - 5 comments
Labels: bug

#318 - Use same version resolution method in `nextstrain setup conda` as `nextstrain update conda`

Issue - State: closed - Opened by victorlin over 1 year ago - 1 comment
Labels: enhancement

#317 - nextstrain view can't connect to host on a Mac inside a Conda environment

Issue - State: open - Opened by huddlej over 1 year ago - 8 comments
Labels: bug

#316 - dev: Update release docs

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 2 comments

#315 - Test compatibility with SingularityCE 4.x series

Issue - State: open - Opened by tsibley over 1 year ago

#314 - dev: Test against the SingularityCE 3.x series in CI

Pull Request - State: closed - Opened by tsibley over 1 year ago - 2 comments

#313 - Avoid fsspec/s3fs 2023.9.1 due to errors caused by `auto_mkdir`

Pull Request - State: closed - Opened by joverlee521 over 1 year ago - 2 comments

#312 - runner.conda: Explicitly install the latest package version during setup

Pull Request - State: closed - Opened by tsibley over 1 year ago - 2 comments

#311 - runner.conda: Plug isolation leaks related to Python

Pull Request - State: closed - Opened by tsibley over 1 year ago