Cromshell

Version Bump (275)

Additions
- [PR265](https://github.com/broadinstitute/cromshell/pull/265) **Added `validate` command**: When invoked performs WDL workflow validation using Cromwell's womtool API and miniwdl. It checks the syntax and type errors in the provided WDL and its associated input JSON file, and it can also optionally handle local imports via miniwdl. If successful, it prints "Validation successful"; otherwise, it prints "Validation failed."
- [PR268](https://github.com/broadinstitute/cromshell/pull/268) **Flatten and submit nested WDLs**: This update addresses a common issue regarding path resolution in nested directory structures when working with WDLs. It introduces a new feature to the submit command, which automatically detects relative imports in workflows, creates a temporary directory, and rewrites WDLs with adjusted imports, making it easier to work with dependencies both within and outside of Terra.
Bug Fixes
- [PR256](https://github.com/broadinstitute/cromshell/pull/256) Fix to have the `version` command print the version
- [PR271](https://github.com/broadinstitute/cromshell/pull/271) Fix to have `metadata` and `slim-metadata` print machine-readable json

We are excited to announce the release of Cromshell 2! This new version of Cromshell brings a number of improvements and new features to the Cromwell job submission experience.

Here are some of the key highlights of Cromshell 2:
- A completely rebuilt codebase in Python, which brings improved reliability, performance, and modularity to the tool.
- Automatic zipping of workflow dependencies when submitting a workflow.
- Integration and unit tests to ensure Cromshell remains a reliable and robust tool.
- Multiple installation options: Cromshell 2 can be installed from source, via Homebrew, or from PyPI.
- A modular architecture that makes adding new functionalities and commands easier.
- Developer documentation that provides guidance on how to add new features and commands to the tool.

The original Cromshell shell script is still available in the legacy_cromshell folder and in the `cromshell1` branch of this repository.It is no longer maintained, but is still available for use. The original Cromshell contains some commands not yet available in Cromshell2,such as `fetch-logs`, `fetch-all`, `notify`, and `cleanup`. These commands will be added to Cromshell2 in the future.

Beta release of Cromshell2

Added commands:

- `alias` - Label the given workflow ID with the given alias
- `counts` - Get the summarized status of all jobs in the workflow (same as execution-status-count)
- `list` - Display a list of jobs submitted through cromshell
- `logs` - List the log files produced by a workflow.
- `timing` - Open the timing diagram in a browser.
- `update-server` - Change the Cromwell server to which new jobs will be submitted.

Added features
- Developer documentation - Step-by-step instructions on adding new commands and their tests to cromshell. 195
- Automatically zip dependency files when submitting a workflow. 214
- Support for users running Cromshell against Cromwell server in Terra workspace. Contributed by the Cromwell team. 208

Alpha release of Cromshell2
This is a rewrite in python which is currently not feature complete with the original. You can view it and contribute in the [cromshell_2.0](https://github.com/broadinstitute/cromshell/tree/cromshell_2.0) branch.

Contains the following commands:
- abort - Abort a running workflow.
- metadata - Get the full metadata of a workflow.
- slim-metadata - Get a subset of the workflow metadata.
- status - Check the status of a Cromwell job UUID
- submit - Submit a workflow and arguments to the Cromwell Server

Please see the Please see the [README](https://github.com/broadinstitute/cromshell/tree/cromshell_2.0#readme) for python installation instructions.

Bug fix release.
ad30776 Fixes `cost` and `detailed cost` queries for new billing setup as of 2022 Aug 11 (219)
e119c23 Add note about cromshell 2 alpha to readme (211)
bb9a1b1 Fixing issue where tasks would be incorrectly labeled as failed. (190)