Fix option handling in pipeline.jl

[suvayu]

Resolves the confusion among the options.

The only "automatic" behaviour is when the source is a file, and no table name has been provided. In that case, it generates a table name by removing special characters from the filename. If tmp=true, the generated table name has a t_* prefix.

name	tmp	remarks
non-empty	as provided
empty	true	table name: t_<safe_filename>
empty	false	table name: <safe_filename>

All other options work independently:

• name::String sets the table name
• tmp::Bool creates the table as a temporary in-memory table
• show::Bool returns the created table as a dataframe

Also refactor most of the test suite to isolated tests as much as possible. Some are unavoidable, since they need some existing state (e.g. a base table), and there is no nice way to do fixtures.

Related issues

Closes #31

Checklist

• I am following the contributing guidelines
• Tests are passing
• Lint workflow is passing
• Docs were updated and workflow is passing

[codecov]

Codecov Report

Attention: Patch coverage is 83.33333% with 3 lines in your changes missing coverage. Please review.

Project coverage is 69.14%. Comparing base (78646dd) to head (06d82e3).

Files	Patch %	Lines
src/pipeline.jl	83.33%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #70      +/-   ##
==========================================
+ Coverage   68.86%   69.14%   +0.28%     
==========================================
  Files           7        7              
  Lines         273      269       -4     
==========================================
- Hits          188      186       -2     
+ Misses         85       83       -2     

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[abelsiqueira]

Thanks for the PR. I've made a few, mostly small, comments.
There are some new lines not covered in the tests (when length(name) == 0), e.g., in set_tbl_col. Can you add a small test for these too?
Otherwise, looks good to me.

[abelsiqueira]

Oh yeah, also, can you update the title of the PR? Thanks!

[suvayu]

There are some new lines not covered in the tests (when length(name) == 0), e.g., in set_tbl_col

Is there a way I can run the coverage tool and generate the report locally?

[abelsiqueira]

There are some new lines not covered in the tests (when length(name) == 0), e.g., in set_tbl_col

Is there a way I can run the coverage tool and generate the report locally?

Yes, you can use the LocalCoverage.jl package. I don't remember exactly the api, but there is some functions with generate or something like that in the name.

[abelsiqueira]

It's

pkg> activate
pkg> add LocalCoverage

taken from https://github.com/TulipaEnergy/TulipaEnergyModel.jl/blob/main/README.dev.md

[abelsiqueira]

Then

julia> using LocalCoverage
# ]
pkg> activate .
# <backspace>
julia> cov = generate_coverage()

[suvayu]

I don't see any html files. I was hoping to see the line-by-line coverage. Anyway, I can wait for the coverage bot.

[abelsiqueira]

I think our docs are incomplete or I didn't copy-paste enough. There is more info here: https://github.com/JuliaCI/LocalCoverage.jl?tab=readme-ov-file#optional-dependencies
You will need to install lcov to visualize it, apparently.

[abelsiqueira]

Thanks for the update. I've made small code formatting comments, mostly for consistency. Though I am fine either way.

I've also mentioned where the code coverage is failing. On the "Files changes" tab you can see the codecov warnings. That being said, we already have #28 to keep track of the missing coverage, so I am fine with merging this.

Everything else look good, so I will approve it.

[suvayu]

I've also mentioned where the code coverage is failing. On the "Files changes" tab you can see the codecov warnings. That being said, we already have #28 to keep track of the missing coverage, so I am fine with merging this.

Also, these are all in set_tbl_col, and I'm working on #34.