chore(docs): update preprocessing tutorial for using inst.pick() instead of pick_types() by btkcodedev · Pull Request #12326 · mne-tools/mne-python

btkcodedev · 2023-12-26T14:46:37Z

Reference issue

Closes #12158

Updated the tutorial by removing legacy method call of mne.io.Raw.pick_types() to instance.pick()

… pick_types() Updated the tutorial by removing legacy method call of mne.io.Raw.pick_types() to instance.pick()

chore(docs): update preprocessing tutorial for using inst.pick() instead of pick_types()

welcome · 2023-12-26T14:46:39Z

Hello! 👋 Thanks for opening your first pull request here! ❤️ We will try to get back to you soon. 🚴

tutorials/preprocessing/15_handling_bad_channels.py

wmvanvliet · 2023-12-27T11:01:39Z

thanks for taking a stab at this @btkcodedev!

hoechenberger · 2023-12-27T11:18:16Z

Thanks for your contribution! I think the beginning of the sentence must also be adjusted, since we don't pass an "exclude" parameter anywhere as far as I can see

Co-authored-by: Marijn van Vliet <w.m.vanvliet@gmail.com>

hoechenberger · 2023-12-30T08:34:16Z

Thanks, but I don't think the sentence makes too much sense the way it's phrased now. I think it would be better to just write that "pick()" retains the bad channels. It's just how the methods works, not the justification why we used it.

tutorials/preprocessing/15_handling_bad_channels.py

mscheltienne · 2024-01-10T11:27:12Z

@btkcodedev Could you review the sentence modification I proposed and add a changelog entry?
For the chanbgelog entry, you can refer to this section of the contributing guide. You need to add yourself to the author list (alphabetical order) and to add a file in this folder, named 12326.other.rst, describe the change in the file and add yourself as author, e.g.

Short description of the changes, by :newcontrib:Firstname Lastname.

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

Update names.inc

Create 12326.other.rst

btkcodedev · 2024-01-11T02:21:26Z

@mscheltienne Changes done :)

mscheltienne

Thank you @btkcodedev
2 more minor comments and this will be good to merge!

doc/changes/devel/12326.other.rst

doc/changes/names.inc

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

hoechenberger · 2024-01-24T16:37:33Z

@wmvanvliet Could you please review again? Currently your change request (which AFAICT has been addressed) is blocking the merge. Thanks!

drammock

just two small nitpicks from me. Thanks for fixing this!

drammock · 2024-01-24T16:49:36Z

doc/changes/devel/12326.other.rst

@@ -0,0 +1 @@
+Updated the text in the preprocessing tutorial to use :class:`mne.io.Raw.pick()` instead of the legacy :class:`mne.io.Raw.pick_types()`, by :newcontrib:`btkcodedev`.


I'm a little surprised that these cross-refs worked; regardless, it's more accurate to mark these with the :meth: role since they're links to methods (not classes). The parentheses will get added automatically.

Suggested change

Updated the text in the preprocessing tutorial to use :class:`mne.io.Raw.pick()` instead of the legacy :class:`mne.io.Raw.pick_types()`, by :newcontrib:`btkcodedev`.

Updated the preprocessing tutorial to use :meth:`mne.io.Raw.pick` instead of the legacy :meth:`mne.io.Raw.pick_types`, by :newcontrib:`btkcodedev`.

drammock · 2024-01-24T16:51:48Z

tutorials/preprocessing/15_handling_bad_channels.py

 # %%
-# Note that we used the ``exclude=[]`` trick in the call to
-# :meth:`~mne.io.Raw.pick_types` to make sure the bad channels were not
+# Note that the method :meth:`~mne.io.Raw.pick()` default


FYI parentheses get added automatically when you use the :meth: role

Suggested change

# Note that the method :meth:`~mne.io.Raw.pick()` default

# Note that the method :meth:`~mne.io.Raw.pick` default

wmvanvliet

Once @drammock's comments are resolved, LGTM

welcome · 2024-01-25T07:57:29Z

🎉 Congrats on merging your first pull request! 🥳 Looking forward to seeing more from you in the future! 💪

wmvanvliet · 2024-01-25T07:59:16Z

Didn't know there was an automerge in place. Perhaps we can fix @drammock's comments directly in main?

hoechenberger · 2024-01-25T10:09:37Z

Thanks for your contribution, @btkcodedev!!

larsoner · 2024-01-29T17:10:46Z

Somehow there is in mne-tools/mne-python :

$ git fetch upstream
...
 From github.com:mne-tools/mne-python
   03d78f43bf..990ce18d4e  main              -> upstream/main
 * [new branch]            revert-12326-main -> upstream/revert-12326-main

I'm going to delete the revert-12326-main assuming perhaps @wmvanvliet or someone else considered reverting for a minute there. Agree with @wmvanvliet that final comments can be addressed quickly elsewhere, but maybe just as part of another PR when someone opens one (rather than a push to main which is always a bit dicey)

mscheltienne · 2024-01-29T18:22:41Z

@wmvanvliet @larsoner I think I addressed the final comments before going on holidays in a PR, not yet merged, which was blocked by the towncrier job failing.

…ead of pick_types() (mne-tools#12326) Co-authored-by: Marijn van Vliet <w.m.vanvliet@gmail.com> Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@fcbg.ch> Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

btkcodedev added 2 commits December 26, 2023 20:11

chore: update preprocessing tutorial for using inst.pick() instead of…

48cadad

… pick_types() Updated the tutorial by removing legacy method call of mne.io.Raw.pick_types() to instance.pick()

Merge pull request #1 from btkcodedev/chore/updatePreprocessDoc

73bd9db

chore(docs): update preprocessing tutorial for using inst.pick() instead of pick_types()

btkcodedev requested review from agramfort, dengemann and drammock as code owners December 26, 2023 14:46

btkcodedev mentioned this pull request Dec 26, 2023

Small error in interpolation tutorial #12158

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wmvanvliet requested changes Dec 27, 2023

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btkcodedev and others added 2 commits December 30, 2023 12:08

Update tutorials/preprocessing/15_handling_bad_channels.py

b5cf780

Co-authored-by: Marijn van Vliet <w.m.vanvliet@gmail.com>

Update 15_handling_bad_channels.py

f7c59cb

btkcodedev requested a review from wmvanvliet December 30, 2023 06:40

mscheltienne reviewed Jan 10, 2024

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Merge branch 'main' into main

f54a065

btkcodedev and others added 5 commits January 11, 2024 07:40

Update tutorials/preprocessing/15_handling_bad_channels.py

16f6d6c

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

Merge branch 'main' into main

4afcff2

Update names.inc

ea31ce6

Create 12326.other.rst

b0da613

Merge pull request #3 from btkcodedev/patch-1

7818ee4

Update names.inc

btkcodedev requested a review from larsoner as a code owner January 11, 2024 02:20

Merge pull request #2 from btkcodedev/patch-2

808c9af

Create 12326.other.rst

Merge branch 'main' into main

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mscheltienne reviewed Jan 15, 2024

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btkcodedev and others added 3 commits January 20, 2024 20:16

Update doc/changes/devel/12326.other.rst

770fc3e

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

Update names.inc

6a0db7e

Merge branch 'main' into main

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btkcodedev requested a review from mscheltienne January 20, 2024 14:48

trigger cis

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mscheltienne enabled auto-merge (squash) January 22, 2024 11:07

mscheltienne added 2 commits January 23, 2024 19:13

Merge branch 'main' into main

ad8c644

fix typo

6f5408b

drammock approved these changes Jan 24, 2024

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wmvanvliet approved these changes Jan 25, 2024

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mscheltienne merged commit f060e6b into mne-tools:main Jan 25, 2024

mscheltienne mentioned this pull request Jan 25, 2024

Fix sphinx roles and parenthesis #12385

Merged

		@@ -0,0 +1 @@
		Updated the text in the preprocessing tutorial to use :class:`mne.io.Raw.pick()` instead of the legacy :class:`mne.io.Raw.pick_types()`, by :newcontrib:`btkcodedev`.

	Updated the text in the preprocessing tutorial to use :class:`mne.io.Raw.pick()` instead of the legacy :class:`mne.io.Raw.pick_types()`, by :newcontrib:`btkcodedev`.
	Updated the preprocessing tutorial to use :meth:`mne.io.Raw.pick` instead of the legacy :meth:`mne.io.Raw.pick_types`, by :newcontrib:`btkcodedev`.

	# Note that the method :meth:`~mne.io.Raw.pick()` default
	# Note that the method :meth:`~mne.io.Raw.pick` default

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btkcodedev commented Dec 26, 2023

Reference issue

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