Bad error message when `None`s are cast to `File`s with `--no-quant-check`

[ThomasHickman]

If you have a workflow where Nones are cast to a File with --no-quant-check enabled, a non-user friendly stack trace is dumped to the console. For example, for the workflow:

version 1.1

workflow test_workflow {
  output {
    Array[File] result = [None]
  }
}

the output is:

$ miniwdl run --no-quant-check test.wdl
2025-08-05 15:27:04.565 wdl.w:test_workflow workflow start :: name: "test_workflow", source: "test.wdl", line: 3, column: 1, dir: "/Users/user/20250805_152704_test_workflow"
2025-08-05 15:27:04.567 wdl.w:test_workflow miniwdl :: version: "v1.12.1", uname: "Darwin F362Y7KQKP-MAC 24.5.0 Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:29 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T6030 arm64"
2025-08-05 15:27:04.569 wdl.w:test_workflow workflow test_workflow (test.wdl Ln 3 Col 1) failed :: dir: "/Users/user/20250805_152704_test_workflow", error: "FileNotFoundError", node: "output-result", traceback: ["Traceback (most recent call last):", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py\", line 1012, in _workflow_main_loop", "    next_call = state.step(cfg, stdlib)", "                ^^^^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py\", line 292, in step", "    raise exn", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py\", line 289, in step", "    res = self._do_job(cfg, stdlib, job)", "          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py\", line 384, in _do_job", "    v = job.node.expr.eval(env, stdlib=stdlib).coerce(job.node.type)", "        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/Value.py\", line 222, in coerce", "    desired_type, [v.coerce(desired_type.item_type) for v in self.value], self.expr", "                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/Value.py\", line 381, in coerce", "    raise FileNotFoundError()", "FileNotFoundError"]
2025-08-05 15:27:04.570 wdl.w:test_workflow aborting workflow
2025-08-05 15:27:04.571 miniwdl-run  :: error: "FileNotFoundError", node: "output-result", traceback: ["Traceback (most recent call last):", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py\", line 1012, in _workflow_main_loop", "    next_call = state.step(cfg, stdlib)", "                ^^^^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py\", line 292, in step", "    raise exn", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py\", line 289, in step", "    res = self._do_job(cfg, stdlib, job)", "          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py\", line 384, in _do_job", "    v = job.node.expr.eval(env, stdlib=stdlib).coerce(job.node.type)", "        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/Value.py\", line 222, in coerce", "    desired_type, [v.coerce(desired_type.item_type) for v in self.value], self.expr", "                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/Value.py\", line 381, in coerce", "    raise FileNotFoundError()", "FileNotFoundError", "", "The above exception was the direct cause of the following exception:", "", "Traceback (most recent call last):", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/CLI.py\", line 821, in runner", "    rundir, output_env = runtime.run(cfg, target, input_env, run_dir=run_dir, _cache=cache)", "                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/__init__.py\", line 63, in run", "    return entrypoint(cfg, exe, inputs, **run_kwargs)  # type: ignore", "           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py\", line 934, in run_local_workflow", "    outputs = _workflow_main_loop(", "              ^^^^^^^^^^^^^^^^^^^^", "  File \"/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py\", line 1113, in _workflow_main_loop", "    raise wrapper from exn", "WDL.runtime.error.RunFailed: workflow test_workflow (test.wdl Ln 3 Col 1) failed"], dir: "/Users/user/20250805_152704_test_workflow"

Here's what the stacktrace looks like with proper formatting:

Traceback (most recent call last):
  File "/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py", line 1012, in _workflow_main_loop
    next_call = state.step(cfg, stdlib)
                ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py", line 292, in step
    raise exn
  File "/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py", line 289, in step
    res = self._do_job(cfg, stdlib, job)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py", line 384, in _do_job
    v = job.node.expr.eval(env, stdlib=stdlib).coerce(job.node.type)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/Value.py", line 222, in coerce
    desired_type, [v.coerce(desired_type.item_type) for v in self.value], self.expr
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/Value.py", line 381, in coerce
    raise FileNotFoundError()
FileNotFoundError

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/CLI.py", line 821, in runner
    rundir, output_env = runtime.run(cfg, target, input_env, run_dir=run_dir, _cache=cache)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/__init__.py", line 63, in run
    return entrypoint(cfg, exe, inputs, **run_kwargs)  # type: ignore
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py", line 934, in run_local_workflow
    outputs = _workflow_main_loop(
              ^^^^^^^^^^^^^^^^^^^^
  File "/Users/user/.local/pipx/venvs/miniwdl/lib/python3.12/site-packages/WDL/runtime/workflow.py", line 1113, in _workflow_main_loop
    raise wrapper from exn
WDL.runtime.error.RunFailed: workflow test_workflow (test.wdl Ln 3 Col 1) failed