Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nextstrain/cli issues and pull requests

#310 - view: Respect HOST and PORT as defaults for --host and --port

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

#309 - Python user site directory leaks into Conda runtime

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

#308 - AWS Batch job control

Pull Request - State: closed - Opened by tsibley over 1 year ago - 5 comments

#307 - Uncaught ImmatureSignatureError: The token is not yet valid (iat)

Issue - State: closed - Opened by corneliusroemer over 1 year ago - 6 comments
Labels: bug

#306 - Ellipsis type; fix broken CI

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

#305 - No download? No build dir? No problem!

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

#304 - Integrate AWS Batch set up and usage doc with runtime doc

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

#303 - Improved and expanded runtime documentation

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

#301 - runner.conda: Bump Micromamba to 1.1.0

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

#300 - `nextstrain update conda` fails silently

Issue - State: closed - Opened by joverlee521 over 1 year ago - 4 comments
Labels: bug

#299 - Docs and command help improvements

Pull Request - State: closed - Opened by tsibley over 1 year ago - 5 comments

#298 - Minor doc fixes

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

#297 - Use central reusable workflow for building docs

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

#296 - dev: Work around issue in CI with Python 3.7.17 on macOS

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

#295 - [batch] ZIP archive of build dir is stored without compression

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

#294 - pyparsing 3.1.0 fix

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

#293 - pyparsing 3.1.0 causing test failures in Markdown image inlining

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

#292 - runner.docker: Use more precise example commands in check-setup failure messages

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

#291 - view: Wait for Auspice to start responding before opening the browser

Pull Request - State: closed - Opened by tsibley over 1 year ago - 3 comments

#290 - ci: Fix silent failure to run pytest on Windows

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

#289 - Environment variables

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

#288 - Improve runtime documentation

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

#287 - Revert "Require docutils <0.16 in dev deps to avoid a version conflict"

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

#286 - runner.conda: Explicitly handle our package versions which are invalid by PEP-440

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

#285 - `nextstrain update conda` in 7.0.0 can error with "Invalid version"

Issue - State: closed - Opened by tsibley over 1 year ago - 13 comments
Labels: bug

#284 - Pyright failures with 1.1.309

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

#283 - Singularity compatibility fixes

Pull Request - State: closed - Opened by tsibley over 1 year ago - 8 comments

#282 - ENH: Detect and warn user if their environment deviates from nextstrain-base

Issue - State: closed - Opened by corneliusroemer almost 2 years ago - 1 comment
Labels: enhancement

#281 - Fix Pyright errors

Pull Request - State: closed - Opened by joverlee521 almost 2 years ago - 1 comment

#280 - runner.conda: Explicitly get latest `main` version

Pull Request - State: closed - Opened by joverlee521 almost 2 years ago - 1 comment

#279 - Docker runner assumes the Docker Hub (docker.io) registry

Issue - State: open - Opened by tsibley almost 2 years ago - 4 comments
Labels: bug

#278 - Standalone installer parity

Pull Request - State: closed - Opened by victorlin almost 2 years ago - 3 comments

#277 - standalone-installer-windows: Use call operator (&) instead of Invoke-Expression

Pull Request - State: closed - Opened by victorlin almost 2 years ago - 2 comments

#276 - Installation fails when there is a space in the path

Issue - State: closed - Opened by victorlin almost 2 years ago - 1 comment
Labels: bug, windows

#275 - Add newline before eval command

Pull Request - State: closed - Opened by victorlin almost 2 years ago

#274 - Read-only filesystem errors from Snakemake in Singularity runtime

Issue - State: closed - Opened by tsibley almost 2 years ago - 2 comments
Labels: bug

#273 - authn: Allow override of Cognito user pool and client ids by environment variables

Pull Request - State: closed - Opened by tsibley almost 2 years ago - 1 comment

#272 - [build] `--cpus` isn't passed to thru when using `--exec`

Issue - State: open - Opened by corneliusroemer almost 2 years ago - 5 comments
Labels: bug

#271 - `Your request was too big` error on stock RSV repo build via aws-batch

Issue - State: open - Opened by corneliusroemer almost 2 years ago - 7 comments
Labels: bug

#270 - Auto-trigger Docker and Conda runtime builds on CLI releases

Issue - State: open - Opened by corneliusroemer almost 2 years ago
Labels: enhancement

#269 - Add command to self-upgrade

Issue - State: open - Opened by corneliusroemer almost 2 years ago - 3 comments
Labels: enhancement

#268 - Shellcheck

Pull Request - State: closed - Opened by tsibley almost 2 years ago

#267 - `nextstrain update singularity` throws error about OCI indexes with Singularity 2.6 and 3.5.3

Issue - State: closed - Opened by tsibley almost 2 years ago - 13 comments
Labels: bug

#266 - [update] Allow downgrades during `nextstrain update conda`

Pull Request - State: closed - Opened by tsibley almost 2 years ago - 12 comments

#265 - Confusing log message "runtime updated" when nothing was changed

Issue - State: open - Opened by corneliusroemer almost 2 years ago - 3 comments
Labels: bug

#264 - BUG: `nextstrain update conda` doesn't seem to update to latest available conda-base

Issue - State: closed - Opened by corneliusroemer almost 2 years ago - 18 comments
Labels: bug

#261 - botocore 1.28.0 compat

Pull Request - State: closed - Opened by tsibley almost 2 years ago - 1 comment

#260 - remote.nextstrain_dot_org: Fix uninterpolated placeholder in error message

Pull Request - State: closed - Opened by tsibley almost 2 years ago

#259 - argparse: Restore --help and --help-all difference on Python ≥3.10

Pull Request - State: closed - Opened by tsibley almost 2 years ago

#258 - dev: Run CI every day on a schedule to catch external breaking changes

Pull Request - State: closed - Opened by tsibley almost 2 years ago

#256 - Bump minimum Python version from 3.6 to 3.7

Pull Request - State: closed - Opened by corneliusroemer almost 2 years ago - 2 comments

#255 - When using `--aws-batch`, the `--image` argument is ignored

Issue - State: closed - Opened by corneliusroemer almost 2 years ago - 2 comments
Labels: bug

#254 - ENH: Print docker image used at beginning of aws-batch jobs

Issue - State: open - Opened by corneliusroemer almost 2 years ago - 2 comments
Labels: enhancement

#253 - [batch] Improvements when attaching to completed jobs

Pull Request - State: closed - Opened by tsibley almost 2 years ago - 2 comments

#252 - standalone-installer-unix: Check for Rosetta 2 in a way that works on macOS 11 too

Pull Request - State: closed - Opened by tsibley about 2 years ago - 3 comments

#251 - Windows: Snakemake arguments with file paths containing backslashes produce file not found errors

Issue - State: open - Opened by huddlej about 2 years ago
Labels: bug, windows, papercut

#250 - Doc updates

Pull Request - State: closed - Opened by tsibley about 2 years ago

#249 - Improve usage of setup-miniconda

Pull Request - State: closed - Opened by victorlin about 2 years ago - 16 comments

#248 - Singularity runtime

Pull Request - State: closed - Opened by tsibley about 2 years ago - 9 comments

#247 - standalone-installer-unix: Error if Rosetta 2 is not enabled on arm64 Macs

Pull Request - State: closed - Opened by tsibley about 2 years ago - 5 comments

#245 - CI fails due to change in Python 3.6 deprecation warning from cryptography

Issue - State: closed - Opened by tsibley about 2 years ago - 1 comment
Labels: bug

#244 - view: Fix --open so it works when using our standalone executable

Pull Request - State: closed - Opened by tsibley about 2 years ago

#243 - Support older glibc versions (e.g. CentOS 7) for standalone installations

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

#242 - `nextstrain view` error message with standalone CLI

Issue - State: closed - Opened by joverlee521 about 2 years ago - 17 comments
Labels: bug

#241 - standalone-installer-unix: Check we can exec the installed binary…

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

#240 - view: Support narratives

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

#239 - Fix CI (again)

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

#238 - remote.nextstrain_dot_org: Handle 400 Bad Request errors

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

#237 - Fix CI

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

#235 - remote.nextstrain_dot_org: Embed images into narratives on upload

Pull Request - State: closed - Opened by tsibley about 2 years ago - 19 comments

#234 - Nexstrain CLI standalone installation fails on EC2 Amazon Linux 2

Issue - State: closed - Opened by hannahhanle over 2 years ago - 5 comments
Labels: bug

#233 - runner.conda: Bump Micromamba version from 0.27.0 to 1.0.0

Pull Request - State: closed - Opened by tsibley over 2 years ago - 4 comments

#232 - shell: Ensure the history file always exists

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

#231 - [shell] shell-history does not exist for Docker

Issue - State: closed - Opened by joverlee521 over 2 years ago - 4 comments
Labels: bug

#230 - ENH: Add `nextstrain update --all` (or `all`) command or support multiple arguments

Issue - State: open - Opened by corneliusroemer over 2 years ago - 1 comment
Labels: enhancement

#228 - Use our new nextstrain-base Conda meta-package

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

#227 - ENH: Output commit hash of the workflow repo used when using repo actions to submit

Issue - State: closed - Opened by corneliusroemer over 2 years ago - 2 comments
Labels: enhancement

#225 - DOC: Mention disk space requirements for managed conda-runtime and docker

Issue - State: closed - Opened by corneliusroemer over 2 years ago - 2 comments
Labels: documentation

#224 - Rename "native" runtime/runner to "ambient"

Pull Request - State: closed - Opened by tsibley over 2 years ago

#223 - Add Conda runtime to our CI integration tests

Pull Request - State: closed - Opened by tsibley over 2 years ago - 11 comments

#222 - runner.docker: Initial, minimal `setup` support

Pull Request - State: closed - Opened by tsibley over 2 years ago

#221 - RFD: `remote upload`'s use of filenames

Issue - State: closed - Opened by tsibley over 2 years ago - 8 comments
Labels: needs discussion

#220 - [setup] Docker runtime support

Issue - State: open - Opened by tsibley over 2 years ago - 1 comment
Labels: enhancement

#219 - [batch] exclude directories for upload

Issue - State: closed - Opened by jameshadfield over 2 years ago - 9 comments
Labels: enhancement, priority: high

#218 - Managed Conda runtime

Pull Request - State: closed - Opened by tsibley over 2 years ago - 29 comments

#217 - Standalone archive installers

Pull Request - State: closed - Opened by tsibley over 2 years ago - 22 comments

#216 - check-setup: Allow --set-default to optionally take a choice

Pull Request - State: closed - Opened by tsibley over 2 years ago - 1 comment

#215 - build: Support advanced globbing features in --download patterns

Pull Request - State: closed - Opened by tsibley over 2 years ago

#214 - ENH: Use brotli compression by default if possible for nextstrain.org requests

Issue - State: open - Opened by corneliusroemer over 2 years ago - 1 comment
Labels: enhancement

#213 - remote download: Use more of the resource path in the local filename

Pull Request - State: closed - Opened by tsibley over 2 years ago

#212 - Use nextstrain.org for standalone installation archive URLs

Pull Request - State: closed - Opened by tsibley over 2 years ago

#211 - dev: Stop using macOS 10.15 runners in CI

Pull Request - State: closed - Opened by tsibley over 2 years ago - 9 comments