pepkit / peppy

Project metadata manager for PEPs in Python
https://pep.databio.org/peppy
BSD 2-Clause "Simplified" License
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`ComposeError` thrown loading PEP #373

Closed nleroy917 closed 2 years ago

nleroy917 commented 2 years ago

Attempting to load the following PEP config file throws an uncaught ComposeError from peppy. Stack trace:

yaml.composer.ComposerError: found undefined alias 'baz'
  in "<my_path_to_config_file>", line 10, column 8

These are the contents of the configuration file:

pep_version: "2.0.0"
sample_table: sample_table.csv
output_dir: $HOME/hello_looper_results
pipeline_dir: $HOME/pipeline_dir

project_modifiers:
  import:
    - project_config1.yaml

timer: *baz

I can catch this error on my end, but seeing as it's being thrown from within Peppy, I thought I'd open an issue here.

nsheff commented 2 years ago

are you trying to define a yaml alias? is that a valid yaml file?

the error is coming from the yaml parser, which is saying your yaml file is not well formed.

nleroy917 commented 2 years ago

I did not write this configuration file. It's pulled directly from the examples repo.

nsheff commented 2 years ago

@stolarczyk was your goal with this config file to test yaml aliases?

Nevermind, that was my example. I remember now, I was experimenting with node aliases.

nsheff commented 2 years ago

I fixed the example so it's valid yaml now.