Introducing Pytest

[pslacerda]

This is my attempt to develop tests direct on the script source.

[JarrettSJohnson]

A bit hard to follow this PR. Changes seem to be mostly redundant with #163 . I assume that the documentation remove is orthogonal to the goals of this PR (#162), thus the changes should be removed.

I suggest creating a PR that does the script movement separately, and create a separate PR based off of those changes (to which you can rebase again when they're merged).

This PR probably also (partially) addresses issue #133 .

[speleo3]

Adding to what Jarrett said: I would appreciate a more comprehensive pull request description, including goals, scope, design, side-effects. E.g.:

• Goal: Implement Testing scripts & plugins #133
• Scope: All "scripts"
• Out-of-scope: plugins
• Design:
  • test_* functions are added directly to the script files like D unittest blocks.
  • All scripts moved to "scripts" because a valid Python identifier is required to PyTest collect tests (not sure). It does importing.
  • "scripts" added to PYTHONPATH so scripts can import each other (was required for "aKMT_Lys_pred.py"
• Side-effect: All PyMOLWiki script links need updating, possibly by enhancing logic in https://pymolwiki.org/index.php/Template:Infobox_script-repo

[pslacerda]

@JarrettSJohnson, I cleaned up the PRs, they're not redundant anymore.

Thanks @speleo3, I'll be more educated next time.

[JarrettSJohnson]

The side-effect that Thomas mentioned is perhaps the one that I'm most concerned about. Do you have a plan for updating the links on PyMOLWiki? I assume that doing all of them at once is probably not feasible? Would it be better to just select/migrate a few representative scripts at a time?

[pslacerda]

The reason I moved the scripts to a "package" named "scripts" was because Pytest couldn't collect all tests. In fact, only a single script crashed the test collection, and it was because of importing "findseq.py".

Pymol-script-repo/aKMT_Lys_pred.py

Lines 14 to 15 in 0251a56

	# From Pymol-script repo: https://pymolwiki.org/index.php/Findseq
	import findseq

Maybe with pytest.importorskip it could skip the offending import. Maybe is useful to make possible scripts/modules "friends" by just importing them, but is used on the single occasion mentioned (at least for scripts, I don't analyzed plugins).

Very much sane to convert in batches sensible scripts could give room to edit any pending necessary PyMOL Wiki changes. But to edit all links in a single batch is also feasible because of https://wiki.pymol.org/index.php/Category:Pymol-script-repo, I guess.

[JarrettSJohnson]

Ah right. I forgot/missed the part that PyMOLWiki creates these link automatically.

[speleo3]

I'm not strictly against moving scripts to a "scripts" folder, certainly would improve tidiness of this repo.

But to prove that it's possible without moving files, I created #164

There is no problem with importing "findseq" from aKMT_Lys_pred.py because I added pythonpath = . to pytest.ini

[pslacerda]

Oh, I see, that`s right!

I'm thinking about move scripts manually one by one. What do you think? In the process, maybe I'll convert documentation examples in testable code?

And I`m unsure how to handle psico extensions like AAIndex.

[pslacerda]

Just did the changes on master.