General comments

[strambc]

I have the following comments:

• The name of the format is not FISH Omics File but FISH Omics Format. Please change repo name.
• The top-level README file should (also) contain an overview as found here: https://github.com/4dn-dcic/fish_omics_file/blob/main/docs/source/overview.rst
• How are we going to deal with FOF-CT vs. FOF-GSML? #41
  -- we are going to keep them separate either as two repo or preferentially as 1 well subdivided if that is possible to do while keeping independent versioning
• We have to discuss the overall structure: I think there should be a directory for the actual FORMAT FILES, other files should not be in the same folder. Otherwise, it is confusing. I understand this is done because we are evaluating the read-the-doc route. I think we have to discuss this further.
• For usability (related to my comment below about FOF-CT vs. FOF-GFML) I think tables have to number so that people can find them more easily.
  -- numbers not on the file names but in the index of read-the-doc
  -- maybe change the name "index" to another more intuitive name for people to know that that is where they should look (maybe linked to from README)
• Should the name of the table file reflect Namespace name?
• Would be useful in README to have a graphical schema of the different tables (similar to Slides 3 or 4 in the poster) #23
• Revise MANDATORY vs. RECOMMENDED vs. OPTIONAL vs. CONDITIONALLY REQUIRED #7

[strambc]

@andreacosolo two questions:

FOC-CT vs FOC-GSML?
I unchecked this item because I saw you added information about the difference between the two in the top-level README...
However, the question to me remains about how we point users to FOF-CT vs. FOF-GSML without them having to piece it together one table at a time?
I would favor having two different sub-directories we can link to from the top-level README.
BTW part of this is confusing because I think we are trying to do two things in the same repo:
-provide documentation and instructions
-provide example data tables someone can download and use...

We might want to clarify what is the actual goal.

Numbering tables
Related to what is the use of this repo vs. usability, I think the tables should be numbered so that people know what is essential, what is recommended for each FOF-CT vs. FOF-GSML

[strambc]

@andreacosolo

I did not see a TABLES subdirectory in the source folder.
I thought we decided to do it...

Is this going to be implemented as part of #18 ?

[andreacosolo]

@strambc that's right. The tables folder was added with #18 and contains csv files that generate File Header and Data Columns sections for each data table.