From 8c5f8eac3cd8c46e0bc17ccb88814a25e9db8573 Mon Sep 17 00:00:00 2001 From: Will Turner Date: Sat, 5 Oct 2024 14:03:19 -0700 Subject: [PATCH 1/6] fix broken links --- CITATION.cff | 4 ++++ doc/authors.rst | 1 + doc/whats_new.rst | 2 ++ examples/convert_ieeg_to_bids.py | 4 ++-- examples/convert_mri_and_trans.py | 2 +- 5 files changed, 10 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 4d81d73c1..3997e94ee 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -194,6 +194,10 @@ authors: - given-names: Aaron family-names: Earle-Richardson affiliation: 'Duke University School of Medicine, Department of Neurology' + - given-names: William + family-names: Turner + affilitation: 'Wu Tsai Neurosciences Institute, Stanford University' + orcid: https://orcid.org/0000-0001-8639-9769 - given-names: Alexandre family-names: Gramfort affiliation: 'Université Paris-Saclay, Inria, CEA, Palaiseau, France' diff --git a/doc/authors.rst b/doc/authors.rst index 407bbfc83..4ce710c96 100644 --- a/doc/authors.rst +++ b/doc/authors.rst @@ -49,4 +49,5 @@ .. _Teon Brooks: https://teonbrooks.com .. _Thomas Hartmann: https://github.com/thht .. _Tom Donoghue: https://github.com/TomDonoghue +.. _Will Turner: https://bootstrapbill.github.io/ .. _Yorguin Mantilla: https://github.com/yjmantilla diff --git a/doc/whats_new.rst b/doc/whats_new.rst index f495df826..9aff07da1 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -21,6 +21,7 @@ The following authors contributed for the first time. Thank you so much! 🤩 * `Amaia Benitez`_ * `Kaare Mikkelsen`_ * `Thomas Hartmann`_ +* `William Turner`_ The following authors had contributed before. Thank you for sticking around! 🤘 @@ -57,6 +58,7 @@ Detailed list of changes - When anonymizing the date of a recording, MNE-BIDS will no longer error during `~mne_bids.write_raw_bids` if passing a `~mne.io.Raw` instance to ``empty_room``, by `Daniel McCloy`_ (:gh:`1270`) - Dealing with alphanumeric ``sub`` entity labels is now fixed for :func:`~mne_bids.write_raw_bids`, by `Aaron Earle-Richardson`_ (:gh:`1291`) - When processing subject_info data that MNE Python imports as numpy arrays with only one item, MNE-BIDS now unpacks these, resulting in a correct participants.tsv, by `Thomas Hartmann`_ (:gh:`1310`) +- Fixed broken links in examples 7 and 8 by `Will Turner`_ (:gh:`1316``) ⚕️ Code health ^^^^^^^^^^^^^^ diff --git a/examples/convert_ieeg_to_bids.py b/examples/convert_ieeg_to_bids.py index 74812f627..8d6714799 100644 --- a/examples/convert_ieeg_to_bids.py +++ b/examples/convert_ieeg_to_bids.py @@ -36,8 +36,8 @@ .. _iEEG part of the BIDS specification: https://bids-specification.readthedocs.io/en/latest/modality-specific-files/intracranial-electroencephalography.html .. _appendix VIII: https://bids-specification.readthedocs.io/en/stable/appendices/coordinate-systems.html -.. _background on FreeSurfer: https://mne.tools/dev/auto_tutorials/source-modeling/plot_background_freesurfer_mne -.. _MNE-Python coordinate frames: https://mne.tools/dev/auto_tutorials/source-modeling/plot_source_alignment.html +.. _background on FreeSurfer: https://mne.tools/stable/auto_tutorials/forward/50_background_freesurfer_mne.html +.. _MNE-Python coordinate frames: https://mne.tools/stable/auto_tutorials/forward/20_source_alignment.html """ # noqa: E501 D400 # Authors: The MNE-BIDS developers diff --git a/examples/convert_mri_and_trans.py b/examples/convert_mri_and_trans.py index 807974d82..b2f71c12b 100644 --- a/examples/convert_mri_and_trans.py +++ b/examples/convert_mri_and_trans.py @@ -320,7 +320,7 @@ # .. _coregistration GUI: # https://mne.tools/stable/auto_tutorials/forward/20_source_alignment.html#defining-the-headmri-trans-using-the-gui # .. _mne_source_coords: -# https://mne.tools/stable/auto_tutorials/source-modeling/plot_source_alignment.html +# https://mne.tools/stable/auto_tutorials/forward/20_source_alignment.html # .. _mne_sample_data: # https://mne.tools/stable/documentation/datasets.html#sample # From 953c1fe14e1f1834ba7b26881bc70ce735cbc328 Mon Sep 17 00:00:00 2001 From: Will Turner Date: Sat, 5 Oct 2024 14:06:27 -0700 Subject: [PATCH 2/6] fix name --- doc/authors.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/authors.rst b/doc/authors.rst index 4ce710c96..6a1e42b46 100644 --- a/doc/authors.rst +++ b/doc/authors.rst @@ -49,5 +49,5 @@ .. _Teon Brooks: https://teonbrooks.com .. _Thomas Hartmann: https://github.com/thht .. _Tom Donoghue: https://github.com/TomDonoghue -.. _Will Turner: https://bootstrapbill.github.io/ +.. _William Turner: https://bootstrapbill.github.io/ .. _Yorguin Mantilla: https://github.com/yjmantilla From f3b7a6757c1e9514888f69c5d06ff564b2e5c3ee Mon Sep 17 00:00:00 2001 From: Will Turner Date: Sat, 5 Oct 2024 14:09:31 -0700 Subject: [PATCH 3/6] fix target name --- doc/whats_new.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/whats_new.rst b/doc/whats_new.rst index 9aff07da1..ff5b041c4 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -58,7 +58,7 @@ Detailed list of changes - When anonymizing the date of a recording, MNE-BIDS will no longer error during `~mne_bids.write_raw_bids` if passing a `~mne.io.Raw` instance to ``empty_room``, by `Daniel McCloy`_ (:gh:`1270`) - Dealing with alphanumeric ``sub`` entity labels is now fixed for :func:`~mne_bids.write_raw_bids`, by `Aaron Earle-Richardson`_ (:gh:`1291`) - When processing subject_info data that MNE Python imports as numpy arrays with only one item, MNE-BIDS now unpacks these, resulting in a correct participants.tsv, by `Thomas Hartmann`_ (:gh:`1310`) -- Fixed broken links in examples 7 and 8 by `Will Turner`_ (:gh:`1316``) +- Fixed broken links in examples 7 and 8 by `William Turner`_ (:gh:`1316``) ⚕️ Code health ^^^^^^^^^^^^^^ From ceea8e2fd83baf99857a622bf0b62408e9cb93d9 Mon Sep 17 00:00:00 2001 From: Will Turner Date: Sat, 5 Oct 2024 14:13:12 -0700 Subject: [PATCH 4/6] fix minor formatting --- doc/whats_new.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/whats_new.rst b/doc/whats_new.rst index ff5b041c4..ed1e235b6 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -58,7 +58,7 @@ Detailed list of changes - When anonymizing the date of a recording, MNE-BIDS will no longer error during `~mne_bids.write_raw_bids` if passing a `~mne.io.Raw` instance to ``empty_room``, by `Daniel McCloy`_ (:gh:`1270`) - Dealing with alphanumeric ``sub`` entity labels is now fixed for :func:`~mne_bids.write_raw_bids`, by `Aaron Earle-Richardson`_ (:gh:`1291`) - When processing subject_info data that MNE Python imports as numpy arrays with only one item, MNE-BIDS now unpacks these, resulting in a correct participants.tsv, by `Thomas Hartmann`_ (:gh:`1310`) -- Fixed broken links in examples 7 and 8 by `William Turner`_ (:gh:`1316``) +- Fixed broken links in examples 7 and 8, by `William Turner`_ (:gh:`1316`) ⚕️ Code health ^^^^^^^^^^^^^^ From 921cdfec3d3b054ce9e4c626eedbf9b6a8d7cde3 Mon Sep 17 00:00:00 2001 From: Will Turner Date: Sat, 5 Oct 2024 14:25:26 -0700 Subject: [PATCH 5/6] fix CITATION file --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 3997e94ee..2a06da3b4 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -197,7 +197,7 @@ authors: - given-names: William family-names: Turner affilitation: 'Wu Tsai Neurosciences Institute, Stanford University' - orcid: https://orcid.org/0000-0001-8639-9769 + orcid: 'https://orcid.org/0000-0001-8639-9769' - given-names: Alexandre family-names: Gramfort affiliation: 'Université Paris-Saclay, Inria, CEA, Palaiseau, France' From 50def25d9900e5b4c661d7bf6db066a2e2b5a2b5 Mon Sep 17 00:00:00 2001 From: Will Turner Date: Sat, 5 Oct 2024 14:27:45 -0700 Subject: [PATCH 6/6] fix typo --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 2a06da3b4..0d585b07e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -196,7 +196,7 @@ authors: affiliation: 'Duke University School of Medicine, Department of Neurology' - given-names: William family-names: Turner - affilitation: 'Wu Tsai Neurosciences Institute, Stanford University' + affiliation: 'Wu Tsai Neurosciences Institute, Stanford University' orcid: 'https://orcid.org/0000-0001-8639-9769' - given-names: Alexandre family-names: Gramfort