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

13

### Scope Computers with `/bin/bash` version

victorlin

Show progress during `check-setup`

1

`nextstrain check-setup` takes almost a minute despite having a fast M1 Pro. There's no progress indicator which might be confusing to users who are running it for the first time....

corneliusroemer

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

4

Nextstrain CLI is currently provided in our managed runtimes, but this "CLI-ception" comes with some odd behavior. It's only noticeable in a few commands related to runtime management (`setup`, `update`)...

victorlin

WIP! - [ ] Document new remote behaviour in doc pages outside of command help - [ ] Document authn flow as a development doc

tsibley

Pass AWS credentials from standard file to Docker

1

### Context Several modes of the CLI support AWS credential defined in the standard `~/.aws/credentials` file including [the AWS Batch mode](https://docs.nextstrain.org/projects/cli/en/stable/aws-batch/#aws-credentials) and [nextstrain remote actions](https://github.com/nextstrain/cli/blob/b7b8aef54540e70b34252eb2aa0ee6ebc375a9c4/nextstrain/cli/remote/s3.py#L38-L40) outside of Docker. These credentials...

huddlej

[aws batch] Progress meter for build dir upload/download

3

It'd be nice to add a [tqdm](https://tqdm.github.io/) progress meter for build dir upload/download when running `nextstrain build --aws-batch`. I think this is only worth it if relatively easy (which it...

tsibley

Unhandled exception when renewing login from a different Cognito user pool

1

### Current Behavior ```sh # Start local nextstrain.org server # Log in to the testing Cognito user pool export NEXTSTRAIN_DOT_ORG=http://localhost:5000 export NEXTSTRAIN_COGNITO_USER_POOL_ID="$(jq -r .COGNITO_USER_POOL_ID ../nextstrain.org/env/testing/config.json)" export NEXTSTRAIN_COGNITO_CLI_CLIENT_ID="$(jq -r .OAUTH2_CLI_CLIENT_ID ../nextstrain.org/env/testing/config.json)"...

victorlin

ENH: Add verbose output to `nextstrain remote` (and potentially other CLI commands)

9

### Context I'm getting an error when uploading but it's not clear what the issue is from the messages I'm getting. I feel like it would be helpful to have...

corneliusroemer

Originally from @tsibley in https://github.com/nextstrain/cli/pull/330#discussion_r1396150186 > This addition is just fine, but seeing it and the existing additions above it reminds me that this module should probably be instantiating its...

joverlee521

config: Add context manager support for combining load() and save()

1

From @tsibley on the topic of improvements to [config](https://github.com/nextstrain/cli/blob/master/nextstrain/cli/config.py) > One thing that might be nice in the future is context manager support for combining `load()` and `save()` , e.g....

kairstenfay