Miniwdl

Latest version: v1.12.0

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0.8.0

`miniwdl run`

* File inputs provided as `s3://` URIs can be downloaded automatically without an extra plugin.
* [opt-in configuration to detect host's AWS credentials](https://github.com/chanzuckerberg/miniwdl/blob/c95fd96480877ebb8efb3fc385a80dda2a0b23bc/WDL/runtime/config_templates/default.cfg#L105-L112)
* otherwise an EC2 instance profile can be assumed, or public S3 URIs are always accessible
* adds to existing support for public `gs://` and web URIs.
* The generated folder of symlinks to output files is renamed from `output_links/` to `out/` for brevity.
* For now an `output_links/`→`out/` symlink appears as well; this backwards-compatibility feature will be removed in the future.
* Experimental [call caching can be enabled](https://miniwdl.readthedocs.io/en/latest/runner_reference.html#task-output-cache-experimental).
* This feature will continue maturing in subsequent versions, probably invalidating existing cached results.

`miniwdl check`

* On syntax or typechecking error, suggest adding WDL version declaration if absent.

`WDL` package

* Each node in the abstract syntax tree returned by `WDL.load()` now has a `parent` attribute, via which one can navigate from any node back up to the root `WDL.Document`.

`miniwdl cromwell`

* Retired per 351

0.7.5

`miniwdl run`

* improve JSON input validation error messages (389)
* `-i input.json` accepts YAML as well as JSON (non-standard feature)
* speed up task directory postprocessing on network file systems
* expanded [documentation](https://miniwdl.readthedocs.io/en/latest/)

`WDL` package

* development library functions `suffix()` `quote()` `squote()` (https://github.com/openwdl/wdl/pull/362 #379 patmagee)
* development grammar removes certain string interpolation options and adds `sep()` function (https://github.com/openwdl/wdl/pull/229 #381 illusional)
* fix `WDL.Value.rewrite_files()` on compound values that use the same `File` value multiple times
* `size()` honors unnecessary 'B' unit for bytes

`miniwdl cromwell`

**Deprecation notice:** `miniwdl cromwell` will be retired in the near future (351)

0.7.4

`miniwdl run`

* Terminal logging displays a bottom "status bar" with the elapsed time, tasks finished/ready/running, and their CPU and memory reservations. Black terminal background suggested for optimal experience.
* For use with log collectors, `--log-json` writes logs in JSON instead of the default format, affecting both the standard error stream and log files left in the run directory.

`miniwdl check`

* New `MissingVersion` warning on documents that don't begin by declaring the WDL language version (and therefore default to the trending-obsolete draft-2)

`WDL` package

* [`WDL.Document.wdl_version`](https://miniwdl.readthedocs.io/en/latest/WDL.html#WDL.Tree.Document.wdl_version) exposes the declared language version, if any

`miniwdl cromwell`

**Deprecation notice:** `miniwdl cromwell` will probably be retired soon, subject to feedback on 351

0.7.3

`miniwdl check`

* Individual lint warnings can be suppressed by a WDL comment containing the string `!WarningName` on the same or following line (183)
* `--no-suppress` displays all lint warnings, even suppressed ones
* `--strict` causes non-zero exit status if any lint warning is displayed (315)

`miniwdl run`

* `_LAST` symbolic link: created alongside each default auto-provisioned, timestamp-named run directory, to make it easier to refer to the most recent run from the command line.
* config option `[task_runtime] memory_limit_multiplier` to set hard limits on container memory usage based on `runtime.memory` (which had been used as a scheduling reservation only)
* fix sporadic race conditions when multiple miniwdl processes run concurrently on the same host/swarm (368 374)

`WDL` package

* Add [`WDL.Document.{source_lines,source_comments}`](https://miniwdl.readthedocs.io/en/latest/WDL.html#WDL.Tree.Document.source_lines) to represent comments in the original source code
* Tighten validation and error messaging for import namespaces (370)

`miniwdl cromwell`

**Deprecation notice:** `miniwdl cromwell` will probably be retired soon, subject to feedback on 351

0.7.2

`miniwdl run`

* make `output_links/` symlinks relative instead of absolute (when the target is within the run directory)
* flock the top-level `workflow.log` file (`task.log` if running a task directly) to help other processes determine if run is still underway
* task parallelism scalability improvements from stress-testing

`WDL` package

* Adds helper `Value.rewrite_files()` and `Value.rewrite_env_files()`

`miniwdl cromwell`

**Deprecation notice:** `miniwdl cromwell` may be retired in the medium-term future; see and comment on 351

0.7.1

`miniwdl run`

* Workflow-level plugin coroutine interface
* Fix errant behavior with multiple installed task plugins
* New [examples](https://github.com/chanzuckerberg/miniwdl/tree/master/examples) of plugins customizing the runner, logging task CPU/memory usage and uploading outputs to cloud storage. (Full plugin API documentation is still needed.)
* Ensure creation of empty `output_links/` folder in run directory, even if task outputs no files
* [Config option](https://github.com/chanzuckerberg/miniwdl/blob/master/WDL/runtime/config_templates/default.cfg) to generate `output_links/` with hardlinks instead of symbolic links (`[file_io] output_hardlinks`)
* Config option to delete task container working directory after completion (`[task_runtime] delete_work`)
* Ensure graceful abort on receipt of SIGPIPE

`WDL` package

* `read_json()` infers WDL types for nested lists/objects, so that WDL accessor expressions can navigate them (320 331 illusional)
* Add [`WDL.Type.unify()`](https://miniwdl.readthedocs.io/en/latest/WDL.html#WDL.Type.unify) supporting this
* Prevent confusion between names *beginning* with `runtime`, `meta`, and `parameter_meta` and actual keywords (363 DavyCats)
* bump [lark-parser](https://github.com/lark-parser/lark) version

`miniwdl localize`

Following last month's deprecation notice, this tool has been repurposed to provide a way to "prime" the [URI file download cache](https://miniwdl.readthedocs.io/en/latest/runner_reference.html#file-download-cache) based on given workflow inputs and/or specified URIs, before actually running the workflow. Doing so can prevent download effort duplication if it's planned to launch multiple concurrent workflows using common reference data URIs.

`miniwdl cromwell`

**Deprecation notice:** `miniwdl cromwell` may be retired in the medium-term future; see and comment on 351

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