Allow adding extra lines to separate commands/parameters

[apcamargo]

This one might be niche, not that useful, and (maybe) annoying to implement. I decided to post it here anyway.

I noticed that when I have several commands, the help dialogue looks very busy and difficult to read:

╭─ Modules ────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│  download-database          Download the latest version of Genomad's database and save it in the DESTINATION         │
│                             directory.                                                                               │
│  annotate                   Predict the genes in the INPUT file (FASTA format), annotate them using Genomad's        │
│                             markers (located in the DATABASE directory), and write the results to the OUTPUT         │
│                             directory.                                                                               │
│  find-proviruses            Find integrated viruses within the sequences in INPUT file using the Genomad markers     │
│                             (located in the DATABASE directory) and write the results to the OUTPUT directory. This  │
│                             command depends on the data generated by the annotate module.                            │
│  marker-classification      Classify the sequences in the INPUT file (FASTA format) based on the presence of         │
│                             Genomad markers (located in the DATABASE directory) and write the results to the OUTPUT  │
│                             directory. This command depends on the data generated by the annotate module.            │
│  nn-classification          Classify the sequences in the INPUT file (FASTA format) using the Genomad neural         │
│                             network and write the results to the OUTPUT directory.                                   │
│  aggregated-classification  Aggregate the results of the marker-classification and nn-classification modules to      │
│                             classify the sequences in the INPUT file (FASTA format) and write the results to the     │
│                             OUTPUT directory.                                                                        │
│  score-calibration          Performs score calibration of the sequences in the INPUT file (FASTA format) using the   │
│                             batch correction method and write the results to the OUTPUT directory. This module       │
│                             requires that at least one of the classification modules was classified previously       │
│                             (marker-classification, nn-classification, aggregated-classification).                   │
│  summary                    Generates a classification report file for the sequences in the INPUT file (FASTA        │
│                             format) and write it to the OUTPUT directory.                                            │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

If I add an additional line to separate the commands, the dialogue looks much better.

╭─ Modules ────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│  download-database          Download the latest version of Genomad's database and save it in the DESTINATION         │
│                             directory.                                                                               │
│                                                                                                                      │
│  annotate                   Predict the genes in the INPUT file (FASTA format), annotate them using Genomad's        │
│                             markers (located in the DATABASE directory), and write the results to the OUTPUT         │
│                             directory.                                                                               │
│                                                                                                                      │
│  find-proviruses            Find integrated viruses within the sequences in INPUT file using the Genomad markers     │
│                             (located in the DATABASE directory) and write the results to the OUTPUT directory. This  │
│                             command depends on the data generated by the annotate module.                            │
│                                                                                                                      │
│  marker-classification      Classify the sequences in the INPUT file (FASTA format) based on the presence of         │
│                             Genomad markers (located in the DATABASE directory) and write the results to the OUTPUT  │
│                             directory. This command depends on the data generated by the annotate module.            │
│                                                                                                                      │
│  nn-classification          Classify the sequences in the INPUT file (FASTA format) using the Genomad neural         │
│                             network and write the results to the OUTPUT directory.                                   │
│                                                                                                                      │
│  aggregated-classification  Aggregate the results of the marker-classification and nn-classification modules to      │
│                             classify the sequences in the INPUT file (FASTA format) and write the results to the     │
│                             OUTPUT directory.                                                                        │
│                                                                                                                      │
│  score-calibration          Performs score calibration of the sequences in the INPUT file (FASTA format) using the   │
│                             batch correction method and write the results to the OUTPUT directory. This module       │
│                             requires that at least one of the classification modules was classified previously       │
│                             (marker-classification, nn-classification, aggregated-classification).                   │
│                                                                                                                      │
│  summary                    Generates a classification report file for the sequences in the INPUT file (FASTA        │
│                             format) and write it to the OUTPUT directory.                                            │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

[ewels]

Should be fairly easy to add as an opt-in thing I think 🤔

[ewels]

Could even give a few different options - blank lines but also horizontal rules / table styles or alternating background colours.

[apcamargo]

Would be awesome!

[ewels]

ok, I just added this functionality in 50d89b7

The new examples/click/10_table_styles.py script shows it in action. The top options table I tried to base roughly on your request.

Note that it's not exactly the same, as in order to set leading=1 you have to use a table box style. Using a box immediately adds a bunch of additional spacing / padding (even if that box is invisible in our case). I removed as much of it as I can, but it's still more spaced:

Hopefully that's ok. If you can figure out how to further reduce the padding, let me know 👍🏻 Alternatively we could add the spacing manually by just dumping a newline in to the help text. More crude, but should have the desired effect.

I figured that people would inevitably request this at custom-group level eventually, so I wrote it in such a way that it can be done on a per-group level too. You can see that in action in examples/click/03_groups_sorting.py

[apcamargo]

Looks perfect! I actually enjoy the extra padding, but I can try to figure out a solution that would allow us to control it.

[ewels]

Great! I set it up with padding and pad_edge already (the latter set to False by default, which the best effect):

rich-click/src/rich_click/rich_click.py

Lines 48 to 49 in 95a3594

	STYLE_OPTIONS_TABLE_PAD_EDGE = False
	STYLE_OPTIONS_TABLE_PADDING = (0, 1)

But I guess that there is still some other cell padding or something creeping in which could be finetuned to get exactly the right effect... But I didn't spend ages looking as I thought it looked ok as it was 😅

Note that some of the table style settings only work when the box is set to something other than None. I probably should have mentioned that in the readme somewhere. That's why I set it to SIMPLE here:

rich-click/examples/click/10_table_styles.py

Lines 3 to 4 in 95a3594

	click.rich_click.STYLE_OPTIONS_TABLE_LEADING = 1
	click.rich_click.STYLE_OPTIONS_TABLE_BOX = "SIMPLE"

[apcamargo]

You're too efficient. I can't keep up hahaha. Thank you so much, @ewels!

I'll try to contribute by figuring out how to fix the other aesthetic bugs that have been bothering me (#35 and #34), but they are much trickier than I was expecting.