Entrypoint

[enryH]

Make report generator executable from anywhere.

[enryH]

I added integration tests for all scripts. I still need to allow the report to be called as vuegen directly (without the python -m call). Looking at the test, I see an error for jupyter which somehow does not lead to the execution failing:

https://github.com/Multiomics-Analytics-Group/vuegen/actions/runs/12429117006/job/34701961965

ERROR: Validation of YAML front matter failed.
ERROR: In file quarto_report/quarto_report.qmd
(line 9, columns 5--19) Field "format" has value kernel: python3, which must instead be no possible value
 8:   jupyter:
 9:     kernel: python3
       ~~~~~~~~~~~~~~~
10: ---
ERROR: Render failed due to invalid YAML.

Is that okay? Do you want to do something about it? If it is an actual error, I would argue that the execution stops and return a non-zero exit code.

[enryH]

@sayalaruano I think its's ready also without the jupyter error. If I read it correctly it's mainly about the default kernel. maybe it Python3 on the runner. Could be tested in a codespace...

[sayalaruano]

Hey @enryH! I took a look at the jupyter error, and got the same result in my local env. It seems that another way to create the ipynb file from the qmd file is with the command:

quarto convert basics-jupyter.qmd

https://quarto.org/docs/tools/jupyter-lab.html

I can add this change in the quarto_reportview.py file. Do you think this will be better, or should we just keep as it is?

[enryH]

Does the error have an impact or not? I think we can discuss this once we tested it a bit... But if you know what should be the result, and the changed command does it, go ahead:)

[sayalaruano]

Hey! Why is it necessary to change the directory to docs? In my local environment, it's working when I execute the program from the base folder, not from docs.

[enryH]

I have to check when I am back, but you could double check in a clean environment within a code space on that branch.

[sayalaruano]

Sure, I will check that out. Thanks!

[sayalaruano]

I just tested in a code space clean environment and it works without changing the directory to docs. Also, I identified some errors with the docx, odt, and pdf formats when converting a df into an image:
OSError: Chrome executable not able to be found on your machine

[enryH]

Well. Then this is another requirement. So which tool relies on chronium? Probably something for the interactive dataframes (itables)

[enryH]

Why cd docs:

1. I wanted to check that the import is not local. vuegen is on the main folder, not jet using the src layout, i.e. moving the packages into a separate src folder.
2. For building the website I will need to have the example report relative to the docs/conf.py file. In the end someone who uses the report generator will have only a folder resembling the docs.

In short: yes we can remove the docs, but let's to it in a separate PR where we change the layout of the repo.

[sayalaruano]

I think that dataframe_image is the one that relies on chromium.
It's ok to remove the cd docs in an independent PR. And should we merge the current PR into the meain with the cd docs?

[enryH]

I will do it now.