Automated feature tracker

[rcannood]

doc/features.md currently lists which functionality has been implemented and is tested.

I think it'd be a good idea to include comments in the source code that lets us automate these checks. Example:

In src/InMemoryAnnData.R:

    X = function(value) {
      if (missing(value)) {
        # trackstatus: class=InMemoryAnnData, slot=X, what=getter, status=done
        private$.X
      } else {
        # trackstatus: class=InMemoryAnnData, slot=X, what=setter, status=done
        private$.X <- private$.validate_matrix(value, "X")
        self
      }
    },

In tests/testthat/test-inMemoryAnnData.R:

# trackstatus: class=InMemoryAnnData, slot=X, what=test_getter, status=done
test_that("read from X", {
  ...
})
# trackstatus: class=InMemoryAnnData, slot=X, what=test_setter, status=done
test_that("write to X", {
  ...
})

The following status could be used:

• done: The implementation is done and should be working
• wip: The implementation is partially complete and should be looked at further or improved upon
• missing: This feature is not implemented yet. If no entry for a particular class or slot can be found, the status is assumed to be missing.

We can search the source files for # trackstatus: and render features.md using the retrieved information.

Thoughts

• Does a package like this already exist?

Alternative notations

# trackstatus: class=InMemoryAnnData, feature=get_X, status=done
# trackstatus: class=InMemoryAnnData, feature=set_X, status=done
# trackstatus: class=InMemoryAnnData, feature=test_get_X, status=done
# trackstatus: class=InMemoryAnnData, feature=test_set_X, status=done

[rcannood]

I created an initial implementation in #55.

• Example of InMemoryAnnData.R

• Resulting features.md.

@lazappi @mtmorgan WDYT?

[rcannood]

I'm going to merge #55 already, but I'm happy to change the way this works in the future. I'll a link to what it looks like atm.

[lazappi]

I guess I'm ok with this for the initial development but I would probably want to remove the comments once most things are implemented. Is the rendered report thing somewhere?

[rcannood]

Here → https://scverse.org/anndataR/articles/features.html

Formatting could definitely be improved, but at least it gets automatically updated when the main branch is updated

[lazappi]

Nice! That's super cool. This might actually be a useful thing to keep longer term so maybe we don't need remove things later like I suggested above.

[rcannood]

😄 Whay!

In that case, I'll consider this issue closed. Happy to revisit things when needed.