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Issues related to Python CLIs

- DirtyRepository: The repository is dirty. Please use the "git" command to clean it.

Context: a renku/ omnibenchmark related command is run and returns an exit status with the above message.

Explanation: Renku (and Omnibenchmark) commands can only be run when there is no unsaved work.

Solution: run renku_save() (Python) or renku save (Bash) and rerun your command.

Context: an error is raised when running the above command and no input data is imported.

Explanation: there might be different reasons; the orchestrator is not set up, there is no input data,...

Solutions: depending on the problem, try the followings:

  • check that an orchestrator is set up for your Omnibenchmark: https://github.com/omnibenchmark/omni_essentials/blob/main/general/benchmark_categories.json

- omni_obj.update_result_dataset() > ParameterError: Invalid parameter value - These datasets don't exist: OR omni_obj.create_dataset() > Dataset zhengmix4eq-filterhvg-pinned already taken. Please use a different name.

Context: Error or warning message when creating a dataset in an Omnibenchmark project

Explanation: the name is already taken or has conflicting dataset name. Typically, a subset of another name that our name matching algorithms could mix. Example: "dataset" vs "dataset-updated".

Solution: change the name: in your config.yml to resolve the conflict; try to avoid spaces and - and rather use _ and more descriptive names.

- GitError: Cannot commit changes

Context: error when running a workflow.

Explanation: It is possible that some files were generated in your data folder, where the output of your workflow will be moved. For reproducibility and tracing purpose, Renku doesn't allow files generation into your output data folder, if they were not generated by a Renku workflow.

Solution: remove the problematic files from your data folder and run again your workflow command.

- FileNotFoundError: [Errno 2] No such file or directory: '/opt/conda/lib/python3.9/site-packages/omniValidator/schemas/...'

Explanation: you are using an older version of omniValidator.

Solution: upgrade omniValidator to > 0.0.19

- InterpreterError: Interpreter could not be identified from extention . Please specify command explicitly.

Context: error when calling get_omni_object_from_yaml('src/config.yaml')

Explanation: your main script likely lacks a complete name (e.g. .R, .py).

Solution: give an explicit name to your script (e.g. run_method.R) and to your config.yaml file (script: field).

- One or several of my data files are only 3 lines long but the initial content is not here

Context: one or several of your data files contain a structure of type: 

version https://git-lfs.github.com/spec/v1
oid sha256:XXXXXXXXXXXXXXXXXXXXXXXXXXXX
size XXXX

Explanation: one or several of your data files have been stored on Git LFS. By default, all large files are pushed there to save memory. More information on the renku documentation.

Solution: on an interactive session, check the fetch automatically LFS data option. In a terminal, you can also fetch the data with git lfs pull.

Last update: December 5, 2023