Is copying conf.py required in Control.py write_config_files()?

[antoniojbt]

Hello,
I'm looking at using external pipelines with cgat-core. As far as I understand:

• For pipeline configuration, only pipeline.yml is needed
• Pipeline report configuration files live elsewhere (ie pipeline_docs)
• Pipeline report files are copied across by specific functions in the corresponding pipeline.py file
  and executed by CGATReport (via Report.py run_report() for instance) or other functions within pipeline.py for Rmd, Jupyter, etc.

It seems conf.py copied by write_config_files() in Control.py was specific to CGATReport. Is this now redundant? Should it better be copied across separately when run_report() is called for instance?
Best,
Antonio

[sebastian-luna-valero]

Hi Antonio,

I agree, and have changed Control.py accordingly in #45

Here is how Report.py uses a default conf.py or sphinxreport.ini:

    if os.path.exists("conf.py"):
        conf_dir = os.path.abspath(".")
    else:
        conf_dir = os.path.join(os.path.dirname(__file__), "configuration")

which looks good to me.

Is there anything else that we need to consider?

Best regards,
Sebastian

[antoniojbt]

Thanks!
Looks good to me too.
Antonio