Fix custom sort by drammock · Pull Request #1391 · sphinx-gallery/sphinx-gallery

drammock · 2024-10-15T17:42:51Z

I think no docs update is needed because now things work the way the docs describe them, but feel free to request changes / push commits if you think I'm wrong about that.

larsoner · 2024-10-15T17:56:42Z

@lucyleeow I did not follow all discussion so I'll let you review, feel free to merge if you're happy. I can look deeper if it would help to have another set of eyes or you're busy though!

drammock

left a few comments to hopefully speed up reviewing

drammock · 2024-10-15T21:00:39Z

sphinx_gallery/gen_rst.py


 def _get_class(gallery_conf, key):
    """Get a class for the given conf key."""
+    from .sorting import FunctionSortKey


nesting required to avoid circular import

drammock · 2024-10-15T21:03:30Z

sphinx_gallery/gen_rst.py

+        if not is_builtin_alias:
+            val = FunctionSortKey(val)


just to spell out the logic of this function:

if it's a string alias of a builtin SortKey class, convert to FQN string

then, if it's a string, check for ".", split, and try to import

if that worked, wrap the imported func in FunctionSortKey (unless it's already a built-in SortKey class)

drammock · 2024-10-15T21:04:47Z

sphinx_gallery/sorting.py



-class FunctionSortKey:
+def FunctionSortKey(func, r=None):


opted for CamelCase on the function name, to avoid changing the API (though if you hate this, it's probably no big deal to change it to snake_case, since it wasn't really working before anyway AFAICT).

If we allow within_subsection_order to take a class instance, then I think this can be reverted and would work on within_subsection_order ?

yep! done in 716b180

drammock · 2024-10-15T21:13:57Z

one other important note: now that FunctionSortKey returns a type (rather than an instance) it will fail sphinx's is_serializable checks. So might be worth highlighting that in the docs / strongly encouraging the use of FQN strings as the preferred way to do custom sorting.

lucyleeow · 2024-10-16T02:51:58Z

Half way through review I realised that I already figured out that subsection_order and minigallery_sort_order worked differently to within_subsection_order, when reviewing #1226. Thus I specifically removed within_subsection_order from the docs (see: https://sphinx-gallery.github.io/stable/configuration.html#custom-sort-keys and my last note: #1226 (comment)

(also which part of the docs were you reading? They can definitely be improved, I was not sure where to put the section on custom sort keys as you can use them for several 'unrelated' configs 😩 )

I do like that this now supports within_subsection_order BUT I think it would no longer work for subsection_order and minigallery_sort_order as these both use _get_callables, which can't be a class.

sphinx-gallery/sphinx_gallery/gen_rst.py

Lines 1698 to 1701 in 9947c26

    
           if inspect.isclass(what): 
        
               raise ConfigError( 
        
                   f"Got class rather than callable instance for {readable}: {what}" 
        
               )

(obviously we need to improve our testing)

Ideally, I think I would love to get rid off _get_class, but this would involve:

internally make the convenience classes (e.g., ExampleTitleSortKey) functions instead of classes, but keep the names as camelcase (since we ask the user to pass as string anyway). I think we only had classes for the stable __repr__ but as we are passing a string now, this is not necessary. I think this would also aid the within_subsection_order and FunctionSortKey problem, as we would no longer be doing:

sphinx-gallery/sphinx_gallery/gen_rst.py

Line 569 in 9947c26

listdir, key=_get_class(gallery_conf, "within_subsection_order")(src_dir)

maybe getting rid of FunctionSortKey altogether (a quick search on github seems to show that it is not really used), it was introduced not long before the serialization stuff.

Sorry @larsoner, have to bring you in here, you'll be able to come up with a better solution than my tired brain.
Also apologies if I have made a mistake somewhere.

drammock · 2024-10-16T17:18:35Z

Thus I specifically removed within_subsection_order from the docs (see: https://sphinx-gallery.github.io/stable/configuration.html#custom-sort-keys and my last note: #1226 (comment)

Ah yes, I somehow missed that within_subsection_order wasn't mentioned in the "Custom Sort Keys" section of the config docs! So my earlier statement of "the docs say you can X but it doesn't work" is not strictly correct.

maybe getting rid of FunctionSortKey altogether (a quick search on github seems to show that it is not really used)

-0.5 from me; this PR came about because I want to use it (on subsection orders) and couldn't get it to work. I'd be content though if passing an FQN string of a sorting function worked on subsection orders. Note that at present (in this PR) FunctionSortKey is getting used internally to convert the imported FQN into a callable class (to parallel the other SortKey classes), so even if removed from the public API, it might still be in the codebase... unless:

I would love to get rid off _get_class

...then maybe FunctionSortKey could go away entirely. I can look into that.

I do like that this now supports within_subsection_order BUT I think it would no longer work for subsection_order and minigallery_sort_order as these both use _get_callables, which can't be a class.

I'll add a test of whether FunctionSortKey still works on subsection_order and minigallery_sort_order, and report back.

lucyleeow · 2024-10-16T22:11:07Z

I completely agree that ideally I would like all 3 configs to be able to take a custom sort key and for them to work similarly.

I think a function and string FQN should work on all 3 but we've just got to get the class thing working.

I thought of getting rid of _get_class because maybe we could get within_subsection_order to work with _get_callables, by changing the convenience classes (e.g., ExampleTitleSortKey) to be functions as they are now given as string. It would also be nice to reduce some complexity in the code. Hopefully I haven't missed something important though.

We can keep FunctionSortKey, I think we can make it work. But I think we'll want to recommend using functions.

Thanks for working on this!

lucyleeow · 2024-10-17T10:18:46Z

Thinking about it more, maybe the convenience classes could be a 'callable' (i.e. class instance) instead of a class. This would allow us to use _get_callables and keep these CamelCased classes as classes, and not have to change them to functions? Instead of init-ing with the src_dir we can just pass it the full path?

The only other thing we would want to make sure works is any existing user's own classes used for within_section_order (as we know the FunctionSortKey does not work). They could have done this by subclassing _SortKey (a search on github for this class was not helpful as I don't think you can do a literal string search over all of github) or making their own class that works the same way. I don't know how common this is but I don't think we could get rid of _get_class without breaking existing users own within_subsection_order classes.

I guess the other option is to loosen, so a class instance or a class are both accepted? Not sure what the best solution is here. I would like to go for getting rid of _get_class but I don't want to break existing users' code/force them to change their code.

Apologies for patchiness, I am on holiday but I will try to keep on top of this.

drammock

OK _get_class is now gone, replaced by a tweaked version of _get_callables. It was quite a game of whack-a-mole running tests locally (mostly because I didn't realize at first all the different ways _get_callables was being used).

Thinking about it more, maybe the convenience classes could be a 'callable' (i.e. class instance) instead of a class. This would allow us to use _get_callables and keep these CamelCased classes as classes, and not have to change them to functions? Instead of init-ing with the src_dir we can just pass it the full path?

What I ended up doing was detecting whether the "callable" was one of our built-in sorter classes, or the class returned by FunctionSortKey, and if so, instantiating them within _get_callables. I think this means that any user-created callable class instances should still work (and IIUC we don't expect users to pass in an actual class right? just instances?)

drammock · 2024-10-17T21:42:25Z

sphinx_gallery/tests/test_gen_gallery.py

+    with pytest.raises(ConfigError, match=r"Unknown string option.*when importing"):
        _fill_gallery_conf_defaults(sphinx_gallery_conf)
    sphinx_gallery_conf = dict(within_subsection_order=1.0)
-    with pytest.raises(ConfigError, match="a fully qualified.*got float"):
+    with pytest.raises(ConfigError, match="must be callable"):


these changes reflect the change from using _get_class to using _get_callables (they had similar but not identical error messages)

drammock · 2024-10-17T22:22:23Z

sphinx_gallery/tests/test_gen_gallery.py

+sphinx_gallery_conf = {
+    "examples_dirs": "src",
+    "gallery_dirs": "ex",
+    "within_subsection_order": FunctionSortKey(custom_sorter),


I can add here

"minigallery_sort_order": FunctionSortKey(custom_sorter), "subsection_order": FunctionSortKey(custom_sorter),

and the test will still pass, but I think that's not especially informative because (IIUC) the site being built by for this test doesn't have subsections / minigalleries? Could use some guidance on how/where to test that FunctionSortKey(my_func) and FQN strings work correctly for minigalleries and subsection ordering... maybe that's already tested here?:

sphinx-gallery/sphinx_gallery/tests/test_full.py

Line 1350 in 9947c26

def test_minigallery_directive(minigallery_tree, test, heading, sortkey):

...but I find that test/parametrization inscrutable, so I'd appreciate some guidance on whether those cases are already covered, and if not, how/where I should add/tweak a test to cover them.

So we could do minigalleries here.

I added a add_rst pytest mark here, which will add a index.rst file in src with the contents of file arg. (This happens in the sphinx_wrapper_app in conftest). See this test for example:

sphinx-gallery/sphinx_gallery/tests/test_gen_gallery.py

Lines 647 to 662 in 13f7e06

@pytest.mark.add_conf(

content="""

sphinx_gallery_conf = {

'examples_dirs': 'src',

'gallery_dirs': 'ex',

}"""

)

@pytest.mark.add_rst(

file="""

Header

======

.. minigallery:: index.rst

"""

)

def test_minigallery_not_in_examples_dirs(sphinx_app_wrapper):

AFAICT we only test FQN string for subsection_order in tinybuild.
It may be a big ask, but what do you think about adding a second subsection to the sphinx_gallery/tests/testconfs/src gallery...?

larsoner · 2024-10-18T17:22:55Z

and IIUC we don't expect users to pass in an actual class right? just instances?

It looks like at least mpl does:

https://github.com/matplotlib/matplotlib/blob/9489b938556b16633591c2e829462b1aa4e4a46e/doc/conf.py#L305

https://github.com/matplotlib/matplotlib/blob/9489b938556b16633591c2e829462b1aa4e4a46e/doc/conf.py#L187

https://github.com/matplotlib/matplotlib/blob/9489b938556b16633591c2e829462b1aa4e4a46e/doc/sphinxext/gallery_order.py#L125

Does that change things?

drammock · 2024-10-18T17:46:52Z

and IIUC we don't expect users to pass in an actual class right? just instances?

It looks like at least mpl does [...] Does that change things?

ah, yes it would. thanks for the tip, I'll rethink this.

drammock · 2024-10-18T17:52:54Z

sphinx_gallery/gen_rst.py

+        # make sure built-in sorter classes get instantiated (so they become callable)
+        if is_custom_sorter or what in BUILTIN_SORTERS:


if we change this conditional to

Suggested change

# make sure built-in sorter classes get instantiated (so they become callable)

if is_custom_sorter or what in BUILTIN_SORTERS:

# make sure classes get instantiated (so they become callable)

if key == "within_subsection_order" and inspect.isclass(what):

then MPL's custom sorter class should work too, and the test suite still passes locally.

I think I am okay with this.

AFAICT custom within_subsection_order config values have to be a class as we previously always instantiated it, before passing it to sort.

This will however, also let you pass a class instance, like the other 2 sort configs, instead of a class that takes the srcdir on init.

done in 716b180

larsoner · 2024-10-21T17:55:50Z

then MPL's custom sorter class should work too, and the test suite still passes locally.

Do you see an easy enough way to modify tinybuild to have mpl's use case? That way we can test the "class" case there but hopefully also test the "class instance" case in more targeted tests like I think you currently have in test_gen_gallery.py

… builtin ones)

drammock · 2024-10-22T22:27:57Z

then MPL's custom sorter class should work too, and the test suite still passes locally.

Do you see an easy enough way to modify tinybuild to have mpl's use case?

Done in 2316166
We lose the fact that tinybuild is testing one of the built-in sorter classes though. Probably not a huge deal.

lucyleeow · 2024-10-23T00:23:14Z

Sorry I got to this late. Would it work to alter sphinx_gallery/tests/testconfs/src to add a subgallery? Is it easy to 'fix' the tests that use sphinx_wrapper_app such that they pass even with a new subgallery?

I only suggest as it would be nice to have more unit tests, as tinygallery tests do get quite convoluted.

drammock · 2024-10-25T20:20:20Z

Sorry I got to this late. Would it work to alter sphinx_gallery/tests/testconfs/src to add a subgallery? Is it easy to 'fix' the tests that use sphinx_wrapper_app such that they pass even with a new subgallery?

I only suggest as it would be nice to have more unit tests, as tinygallery tests do get quite convoluted.

I think I've achieved what you ask in d25c7d5 but please double-check it's what you expected, I'm still not sure I've wrapped my head around your test suite.

lucyleeow · 2024-10-26T21:54:10Z

Yes thats exactly what I was thinking. Just seems like we'd need to update a few more tests, to account for the new subgallery but otherwise seems reasonable. Thank you.

drammock · 2024-10-28T20:41:49Z

ok sorting tests are fixed @lucyleeow (sorry I missed those before, thought I ran full pytest before pushing but I must not have). All green now.

lucyleeow

So sorry about the delay.

Some nits, mostly around testing (and its mostly our fault, e.g., I didn't realise we hardly test subsection_order), otherwise this is looking good.

I think some doc updates should go with this, but I can add them later in a separate PR as there are a few things I want to amend and move around.

lucyleeow · 2024-10-31T06:07:23Z

sphinx_gallery/gen_gallery.py


-    # classes (not pickleable so need to resolve using fully qualified name)
-    _get_class(gallery_conf, "within_subsection_order")  # make sure it works
+    # callable classes (not pickleable so need to resolve using fully qualified name)


I am confused by this comment, maybe we could improve it.

AFAICT, within_subsection_order not does not need to be a class? If it is a class we instantiate it, but otherwise as long as it is a callable, it's fine.

The pickleable part; I think is talking about how we updated to using strings for the builtin sorters for new Sphinx (ref: #1289). I think we could move this to within _get_callables, above:

if what in builtin_aliases: what = f"sphinx_gallery.sorting.{what}"

So maybe we can just amend this comment to:

Suggested change

# callable classes (not pickleable so need to resolve using fully qualified name)

# check `within_subsection_order`

sphinx_gallery/gen_rst.py

lucyleeow · 2024-10-31T06:26:14Z

sphinx_gallery/tests/test_gen_gallery.py

+def _check_order(sphinx_app, key, expected_order=None):
    """Iterates through sphx-glr-thumbcontainer divs and reads key from the tooltip.

    Used to test that these keys (in index.rst) appear in a specific order.


Could we add a line here explaining what expected_order is doing?

lucyleeow · 2024-10-31T06:59:50Z

sphinx_gallery/tests/tinybuild/doc/conf.py

    "backreferences_dir": "gen_modules/backreferences",
    "subsection_order": f"{util_root}.noop_key",
-    "within_subsection_order": "FileNameSortKey",
+    "within_subsection_order": CustomSortKey,


I think it would be nice to keep the string, to make sure this works. Is it possible check the custom class in test_gen_gallery.py now that we have added a subsection?

somehow I missed this comment before, but I think it's now moot? The string-aliases for builtin sorters are now comprehensively tested in test_example_sorting (as are FQN strings of custom funcs, and actual callable functions) so AFAICT it's actually preferable to keep this as-is (since in the parametrized test we only test callable functions, not callable classes).

Yes totally agree, this is good as is.

lucyleeow · 2024-10-31T07:00:33Z

sphinx_gallery/tests/test_gen_gallery.py

+sphinx_gallery_conf = {
+    "examples_dirs": "src",
+    "gallery_dirs": "ex",
+    "within_subsection_order": FunctionSortKey(custom_sorter),


So we could do minigalleries here.

I added a add_rst pytest mark here, which will add a index.rst file in src with the contents of file arg. (This happens in the sphinx_wrapper_app in conftest). See this test for example:

sphinx-gallery/sphinx_gallery/tests/test_gen_gallery.py

Lines 647 to 662 in 13f7e06

@pytest.mark.add_conf(

content="""

sphinx_gallery_conf = {

'examples_dirs': 'src',

'gallery_dirs': 'ex',

}"""

)

@pytest.mark.add_rst(

file="""

Header

======

.. minigallery:: index.rst

"""

)

def test_minigallery_not_in_examples_dirs(sphinx_app_wrapper):

AFAICT we only test FQN string for subsection_order in tinybuild.
It may be a big ask, but what do you think about adding a second subsection to the sphinx_gallery/tests/testconfs/src gallery...?

lucyleeow · 2024-11-01T01:36:00Z

Let me know when you are done and I'll take another look. Thanks again 🙏

drammock · 2024-11-01T17:43:35Z

Let me know when you are done and I'll take another look. Thanks again 🙏

OK I think it's ready! I didn't touch the docs because you said you wanted to tackle that in a separate PR. I did a somewhat bold refactor of the example sorting tests --- there's now just one test, which is parametrized over the different ways of sorting. It's a bit wonky looking because part of the parametrization is itself in a pytest.mark (the add_conf mark) but the pytest.param IDs are really explicit so hopefully it's not too hard to figure out what's going on there.

On the plus side: one of the added tests revealed that it wasn't actually working to set subsection order with a plain list, so I've fixed that too (I checked by removing the ExplicitOrder() wrapper in MNE-Python's docs --- the doc build fails on SG master and succeeds on this PR).

lucyleeow

LGTM, thanks for all your work on this. Especially for fixing the subsection order plain list!

I see a few minigallery directives in the new plot example files. Did you have plans for adding minigallery sort tests? I am very okay with you not doing this though, as you've already done so much work on this PR already.

Otherwise, just a question.

I'll merge in a few days in case @larsoner wants to take a look

lucyleeow · 2024-11-03T09:14:10Z

sphinx_gallery/tests/test_gen_gallery.py

+    The regex below extracts info from that source-of-truth line to check that the
+    thumbnail ordering was correct --- unless `expected_order` is provided, in which
+    case an alternative regex extracts the digit-part of the filename from the crossref,
+    and compares the order of crossrefs to `expected_order`.


Thanks for adding this. I actually did not realise the check was this complicated!

lucyleeow · 2024-11-03T09:16:22Z

sphinx_gallery/tests/test_gen_gallery.py

-    'gallery_dirs': 'ex',
-    'within_subsection_order': "FileSizeSortKey",
-}"""
+_subsection_explicit_order_list = pytest.mark.add_conf.with_args(


I was confused about the with_args so I tested it without (i.e. just pytest.mark.add_conf) and the test seemed to work fine. Is it safer/better to use with_args ?

nope, I just misunderstood the pytest docs. After re-reading, it seems you only need with_args if there's a single positional arg to the custom marker and that single positional arg is itself a callable. I'll push a commit removing the with_args part.

lucyleeow · 2024-11-03T09:32:28Z

sphinx_gallery/tests/tinybuild/doc/conf.py

    "backreferences_dir": "gen_modules/backreferences",
    "subsection_order": f"{util_root}.noop_key",
-    "within_subsection_order": "FileNameSortKey",
+    "within_subsection_order": CustomSortKey,


Yes totally agree, this is good as is.

drammock · 2024-11-04T20:00:39Z

I see a few minigallery directives in the new plot example files. Did you have plans for adding minigallery sort tests?

nope, those were just copy-pasted from existing plot_1.py etc, I wasn't planning anything there.

drammock · 2024-11-04T20:02:20Z

sphinx_gallery/gen_gallery.py

+        subsec_order = gallery_conf.get("subsection_order")
+        if isinstance(subsec_order, list):
+            gallery_conf["subsection_order"] = ExplicitOrder(subsec_order)


this is the change that makes bare lists work for subsection_order (must be wrapped in ExplicitOrder before the call to _get_callables)

lucyleeow · 2024-11-06T22:46:53Z

Thank you @drammock !

in MNE-BIDS doc/conf.py we have: ``` sphinx_gallery_conf["within_subsection_order"] = "mne_bids.utils._example_sorter" ``` But AFAICT this functionality wasn't workign prior to sphinx-gallery/sphinx-gallery#1391 , which was included in the release of sphinx-agallery v0.19 (released Feb 12 2025). https://sphinx-gallery.github.io/stable/changes.html#v0-19-0 Given that v0.19 was released less than 1 year ago, I think it is reasonable to assume that devs/contributors might have a sphinx-gallery version < 0.19 installed locally, in which case building the mne-bids docuemntation will fail, but the reason/solution won't be explicit. So I think that it is best to be explicit about the minimum required sphinx-gallery version we require to be able to successfully build our docs.

* DOC: Add html-noplot recipe to doc/Makefile And we also tweak `make view` so that the built documentation opens regardless of whether it was built with make html or make html-noplot * FIX: Pin sphinx-gallery in MNE-BIDS doc/conf.py we have: ``` sphinx_gallery_conf["within_subsection_order"] = "mne_bids.utils._example_sorter" ``` But AFAICT this functionality wasn't workign prior to sphinx-gallery/sphinx-gallery#1391 , which was included in the release of sphinx-agallery v0.19 (released Feb 12 2025). https://sphinx-gallery.github.io/stable/changes.html#v0-19-0 Given that v0.19 was released less than 1 year ago, I think it is reasonable to assume that devs/contributors might have a sphinx-gallery version < 0.19 installed locally, in which case building the mne-bids docuemntation will fail, but the reason/solution won't be explicit. So I think that it is best to be explicit about the minimum required sphinx-gallery version we require to be able to successfully build our docs.

drammock added 3 commits October 15, 2024 12:36

add failing tests

bfc0373

convert FunctionSortKey to class factory

291787e

make it work with FQNs

7f612ab

larsoner added the bug label Oct 15, 2024

drammock added 2 commits October 15, 2024 15:40

adapt non-building FunctionSortKey test

aae1c4b

fix all the other tests

a14a11c

drammock commented Oct 15, 2024

View reviewed changes

drammock added 5 commits October 17, 2024 14:32

fold _get_class into _get_callables

81f9b18

better name

f70a5bb

refactor away the helper func

53e1c8c

minimize diff

e42a21a

remove single-use variable; simplify conditional

3149d04

drammock commented Oct 17, 2024

View reviewed changes

drammock commented Oct 18, 2024

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drammock mentioned this pull request Oct 18, 2024

Control example order via explicit list, not via sorting titles mne-tools/mne-bids#1321

Merged

7 tasks

drammock added 2 commits October 22, 2024 17:01

revert FunctionSortKey changes; instantiate *any* class (not just our…

716b180

… builtin ones)

test custom sort class in tinybuild

2316166

add subgallery to testconfs

d25c7d5

fix sorting tests

b865038

lucyleeow reviewed Oct 31, 2024

View reviewed changes

drammock added 4 commits October 31, 2024 15:26

add second subsection to testconfs

aa34cfa

move comment

38e2b2b

explain test

aad22e2

parametrize tests and add a test case

17e780e

drammock added 5 commits November 1, 2024 11:58

additional test cases

d0d29bd

add failing test for list-style explicit order

f9caf8b

fix it

f127f74

cleanups

b407fe6

comments

c105328

lucyleeow approved these changes Nov 3, 2024

View reviewed changes

remove with_args

fd6cdfa

remove cruft

7579d56

drammock commented Nov 4, 2024

View reviewed changes

lucyleeow merged commit 7e2adbc into sphinx-gallery:master Nov 6, 2024

This was referenced Nov 7, 2024

DOC Improve custom sort key docs #1401

Merged

MNT Add test for minigallery_sort_order #1402

Merged

drammock deleted the fix-custom-sort branch December 10, 2024 19:46

lucyleeow mentioned this pull request Feb 11, 2025

subsection_order says I must provide a callable but the docs say you can give a list of paths #1432

Closed

seisman mentioned this pull request Feb 13, 2025

Bump to sphinx-gallery>=0.19 and use list in subsection_order and string in within_subsection_order GenericMappingTools/pygmt#3805

Merged

scott-huberty mentioned this pull request Nov 3, 2025

Add html-noplot recipe to doc/Makefile mne-tools/mne-bids#1468

Merged

	@pytest.mark.add_conf(
	content="""
	sphinx_gallery_conf = {
	'examples_dirs': 'src',
	'gallery_dirs': 'ex',
	}"""
	)
	@pytest.mark.add_rst(
	file="""
	Header
	======

	.. minigallery:: index.rst
	"""
	)
	def test_minigallery_not_in_examples_dirs(sphinx_app_wrapper):

		# make sure built-in sorter classes get instantiated (so they become callable)
		if is_custom_sorter or what in BUILTIN_SORTERS:

	# callable classes (not pickleable so need to resolve using fully qualified name)
	# check `within_subsection_order`

Conversation

drammock commented Oct 15, 2024

Uh oh!

larsoner commented Oct 15, 2024

Uh oh!

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drammock commented Oct 15, 2024

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