stxue1 issues

Results 62 issues of


                                            stxue1

Array coerces to String in MiniWDL

The spec of WDL 1.1 says that [compound types cannot be coerced into string](https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#expression-placeholder-coercion), but when I ran [this workflow](https://github.com/DataBiosphere/wdl-conformance-tests/blob/5ebba6121b516067dc0cf3a6c57dfff04ecf7211/tests/array_to_string/array_to_string.wdl), MiniWDL seems to automatically convert any type to String as...

interop

PermissionError when running miniwdl with Docker Desktop on Linux

When running `miniwdl run_self_test` miniwdl fails to chmod the work directories ``` 2023-06-07 12:36:11.862 wdl.w:hello_caller.download0.t:download-aria2c Traceback (most recent call last): File "/home/heaucques/Documents/toil/venv/lib/python3.10/site-packages/WDL/runtime/task.py", line 224, in run_local_task chmod_R_plus(run_dir, file_bits=0o660, dir_bits=0o770) File...

devex

Singularity running as root inside an unprivileged Kubernetes pod fails to extract images

**Version of Singularity** What version of Singularity are you using? Run: ``` $ singularity --version singularity-ce version 4.1.2-jammy ``` **Describe the bug** Extraction with unsquashfs 4.5 in a unprivileged Kubernetes...

bug

needs investigation

`nargs=argparse.REMAINDER` can break config file option parsing

Example: ```python import configargparse parser = configargparse.ArgParser() parser.add_argument("--config", is_config_file_arg=True, default="config.cfg") parser.add_argument('--config_file_option', nargs="*", default=None) # also happens with action="append" and any of its derivatives parser.add_argument("remainder_option", nargs=argparse.REMAINDER, default=None) args = ["test"] options...

Update to Python 3.12

Adds Python 3.12 to CI ## Changelog Entry To be copied to the [draft changelog](https://github.com/DataBiosphere/toil/wiki/Draft-Changelog) by merger: * Add support for Python 3.12 ## Reviewer Checklist * [ ] Make...

TES and seccomp confinement

Is a TES task currently allowed to use all system calls available? If the host kernel has seccomp and the task container is ran with Docker, [all these system calls](https://docs.docker.com/engine/security/seccomp/)...

Expose backend parameter to run container with additional permissions

We want to run some of the [Toil](https://toil.readthedocs.io/) interpreters for WDL and CWL with TES under Funnel. We run TES jobs by running Toil containers, which we then pass a...

enhancement

Feature Request

stxue1