1.13.0 (10 September 2019)
deploycommand no longer requires permission to perform the globally-scoped AWS IAM action
s3:ListAllMyBuckets. Instead, it uses the
HEAD <bucket>S3 API which requires either
s3:ListBucket, which can be scoped to specific buckets in IAM grants, or
s3:HeadBucket, which is globally-scoped but does not reveal bucket names. More details on these IAM actions are in the S3 documentation.
1.12.0 (5 September 2019)
deploycommand now supports files other than JSON data files, such as Markdown narratives, by setting the correct content type on upload.
1.11.2 (3 September 2019)
- This release fixes a regression in the
viewcommand which caused "connection reset" or "empty response" errors. The regression only affected versions 1.11.0 and 1.11.1 of the Nextstrain CLI when used with Auspice 1.38.0 via the
nextstrain/base:build-20190828T223744Zimage. Thanks to Thomas Adams for the excellent bug report!
1.11.1 (30 August 2019)
check-setupcommand no longer errors when Docker isn't installed.
1.11.0 (30 August 2019)
viewcommand now supports
--nativeflag to run in the native ambient environment.
check-setupcommand now supports a
--set-defaultflag to save the first supported environment to the Nextstrain CLI's config file. This means that you don't have to specify
--aws-batch) every time if you don't have/want Docker support.
--verboseflag to the
versioncommand will no longer cause the Docker image to be downloaded when it isn't available locally.
- Describe the somewhat annoying process of how to increase the disk space available to AWS Batch jobs in the AWS Web Console.
1.10.2 (23 August 2019)
- The environment variables used by Augur are now passed through to --docker and --aws-batch builds.
1.10.1 (26 March 2019)
viewcommand now sports a
--portoption to use an alternate port for the viewer.
1.10.0 (22 February 2019)
- Add ability to specify vCPU and memory when running AWS Batch jobs via
--aws-batch-memoryor via specification in
~/.nextstrain/configor via environment variables
NEXTSTRAIN_AWS_BATCH_MEMORY. This requires corresponding proper setup of compute environment in AWS Batch console.
1.9.1 (11 February 2019)
- Restore the modification times of files when unzipping results from an AWS Batch run. This allows Snakemake's dependency resolution to properly determine file staleness, which in turn allows local builds to continue where AWS Batch builds leave off (e.g. running the bulk of the computation on AWS Batch and then iterating on subsequent trivial steps locally).
1.9.0 (8 February 2019)
- Builds run on AWS Batch no longer delete the build dir zip file from S3 or the job log stream from CloudWatch, making it easier to debug and troubleshoot Batch builds. The Batch setup documentation is updated to note that the previously suggested retention policies are now the only thing preventing runaway data storage costs (and thus a must).
- Declare missing dep on setuptools, used via
updatecommands. setuptools nearly always exists already on Python installs, especially when nextstrain-cli is installed using pip, but nearly always is not always.
- Static type checking now passes again thanks to a work around for a mypy bug related to namespace packages.
1.8.1 (21 January 2019)
check-setupcommand now tests if the local Docker image is new enough for this version of the CLI.
1.8.0 (18 January 2019)
Docker images between
build-20190116T000613Z(inclusive) broke the
nextstrain viewcommand. It is fixed in this version of the CLI, 1.8.0, in tandem with new images, starting with
build-20190119T045444Z. If your
viewcommand is broken, running
nextstrain updateand following the instructions to upgrade to version 1.8.0 of the CLI should resolve the issue.
AWS Batch builds now avoid uploading files matching
environment*in the build directory, as such files are commonly used for storing sensitive environment values.
1.7.3 (28 December 2018)
- The automatic check for newer versions of the CLI, which happens on the
check-setupcommands, now produces a better, more-likely-to-work suggested invocation of pip to perform the upgrade.
1.7.2 (28 December 2018)
buildcommand now runs
--printshellcmdsoption for improved log output.
User-provided paths are now resolved strictly—they must exist—on both Python 3.5 and ≥3.6, not just 3.5. This discrepancy was unlikely to result in any noticeable problems because of other existence checks which were performed. Nevertheless, the change is good housekeeping and helps ensure robustness.
updatecommand no longer errors on Python 3.6.0 and 3.6.1 when the
~/.nextstrain/does not exist (for example, when upgrading from CLI versions before 1.7.0). #37
Continuous integration testing now includes a much fuller range of Python versions in order to more quickly catch bugs like the one affecting
Continuous integration testing switched to running the zika-tutorial, a simplified build more suitable for our needs.
1.7.1 (5 December 2018)
shellcommand no longer throws an unexpected exception about a missing
warn()function when a non-existent build directory is given. The user-friendly error is printed instead, as expected.
1.7.0 (26 November 2018)
Builds can now be run remotely on AWS Batch by passing the
--aws-batchflag to the
nextstrain build --helpfor more information. Setup required to support this is documented in
updatecommand now pulls down new images by their
build-*tag instead of tracking the mutable
latesttag. Our build tags are, most importantly, not updated after creation and thus are suitable references for reproducible runs. The output of
nextstrain version --verbosenow includes the specific build tag.
check-setupcommand now tests the amount of memory available to containers and warns if it less than 2GB. This is particularly important on Windows and macOS where Linux containers are run inside a VM on the host. The VM may have limited memory allocated to it, leading to out-of-memory errors in builds.
Installation instructions in the README are now more detailed.
A big picture overview of where the CLI fits into the Nextstrain ecosystem is included in the README for situating newcomers.
The README now refers to Docker Desktop, the new name for Docker Community Edition.
1.6.1 (25 September 2018)
shellcommand announces you're entering the build environment, prints information about mapped volumes, and describes how to leave the environment.
1.6.0 (18 September 2018)
- On Windows, fix an issue where the
shellcommands spawn the
docker runprocess but also immediately return the user to the command-line. For
shell, the situation was weirder still because the user ended up with two command prompts (cmd.exe and bash) but only one appeared to win when reading from the shared stdin.
1.5.0 (4 September 2018)
buildcommand now supports a
--nativeflag to run the build outside of any container image, that is, within the ambient environment. That environment might be provided by conda or a cluster module system or custom installs or some other thing. Docker remains the default, although it may be explicitly specified with
--docker. Other runners are planned for the future. The idea is that the cli as a user-facing tool for Nextstrain is separate from a containerized Nextstrain environment (although the two work well together).
shellcommands now show an abbreviated set of common options when passed
--help. The full set of options is available using
--help-all. The idea is to make the initial output more approachable.
The README now describes how to annotate the type of variable and use other typing features in a way that's compatible with Python 3.5
Package metadata for PyPi is slightly improved.
1.4.1 (11 August 2018)
- Minor updates to README and command help strings
1.4.0 (9 August 2018)
- A new
shellcommand launches an interactive shell (bash) inside the build environment, which is useful for running ad-hoc commands and debugging.
1.3.0 (9 August 2018)
updatecommand now prunes old Docker images after downloading new ones. This functionality relies on our new, labeled images. Older images will have to be manually pruned as a one-time step. See
docker image prunefor more information. Note that locally built images which are tagged nextstrain/base:latest will be pruned when
updateis run. Protect such images by giving them an additional tag.
The versions of the Docker image and individual Nextstrain components in the image are shown when the
versioncommand is run with the
1.2.0 (1 August 2018)
deploycommand supports uploading data files to S3, allowing the complete pathogen build lifecycle to happen using this package.
updatecommands now check if the CLI itself is out of date and could be updated.
- Brief descriptions of the changes in each release are now kept in the
CHANGES.mdfile. You're reading it!
Describe basic development practices for this package in the README.
Commit to semantic versioning, which I'd been neglecting previously when bumping versions.
Static type checking is now supported for a small fraction of the source code and runs clean under mypy. This is included in Travis CI testing. The goal is to add more type annotations going forward.