From 06b5bf3574c3deefc0b5b42386e2f00564065f18 Mon Sep 17 00:00:00 2001 From: Circle Ci Date: Fri, 12 Jul 2024 15:17:06 +0000 Subject: [PATCH] doc updates [skip ci] --- dev/.buildinfo | 2 +- .../auto_examples_python.zip | Bin 100022 -> 100022 bytes .../auto_examples_jupyter.zip | Bin 154541 -> 154541 bytes dev/_modules/index.html | 6 +- dev/_modules/mne_bids/copyfiles.html | 6 +- dev/_modules/mne_bids/dig.html | 6 +- dev/_modules/mne_bids/inspect.html | 6 +- dev/_modules/mne_bids/path.html | 6 +- dev/_modules/mne_bids/read.html | 6 +- dev/_modules/mne_bids/report/_report.html | 6 +- dev/_modules/mne_bids/sidecar_updates.html | 8 +-- dev/_modules/mne_bids/stats.html | 6 +- dev/_modules/mne_bids/utils.html | 12 ++-- dev/_modules/mne_bids/write.html | 16 ++--- dev/_static/documentation_options.js | 2 +- dev/api.html | 6 +- dev/authors.html | 6 +- dev/auto_examples/anonymize_dataset.html | 60 +++++++++--------- dev/auto_examples/bidspath.html | 6 +- dev/auto_examples/convert_eeg_to_bids.html | 8 +-- dev/auto_examples/convert_empty_room.html | 8 +-- dev/auto_examples/convert_group_studies.html | 8 +-- dev/auto_examples/convert_ieeg_to_bids.html | 8 +-- dev/auto_examples/convert_mne_sample.html | 54 ++++++++-------- dev/auto_examples/convert_mri_and_trans.html | 8 +-- dev/auto_examples/convert_nirs_to_bids.html | 8 +-- dev/auto_examples/create_bids_folder.html | 6 +- dev/auto_examples/mark_bad_channels.html | 8 +-- dev/auto_examples/read_bids_datasets.html | 41 ++++++------ .../rename_brainvision_files.html | 8 +-- dev/auto_examples/sg_execution_times.html | 32 +++++----- dev/auto_examples/update_bids_datasets.html | 8 +-- dev/contribute.html | 6 +- dev/generated/cli.html | 6 +- dev/generated/mne_bids.BIDSPath.html | 6 +- dev/generated/mne_bids.anonymize_dataset.html | 6 +- .../mne_bids.convert_montage_to_mri.html | 6 +- .../mne_bids.convert_montage_to_ras.html | 6 +- ...e_bids.copyfiles.copyfile_brainvision.html | 6 +- .../mne_bids.copyfiles.copyfile_bti.html | 6 +- .../mne_bids.copyfiles.copyfile_ctf.html | 6 +- .../mne_bids.copyfiles.copyfile_edf.html | 6 +- .../mne_bids.copyfiles.copyfile_eeglab.html | 6 +- .../mne_bids.copyfiles.copyfile_kit.html | 6 +- .../mne_bids.find_matching_paths.html | 6 +- .../mne_bids.get_anat_landmarks.html | 6 +- .../mne_bids.get_anonymization_daysback.html | 6 +- .../mne_bids.get_bids_path_from_fname.html | 6 +- dev/generated/mne_bids.get_datatypes.html | 6 +- .../mne_bids.get_entities_from_fname.html | 6 +- dev/generated/mne_bids.get_entity_vals.html | 6 +- .../mne_bids.get_head_mri_trans.html | 6 +- dev/generated/mne_bids.inspect_dataset.html | 6 +- .../mne_bids.make_dataset_description.html | 6 +- dev/generated/mne_bids.make_report.html | 6 +- dev/generated/mne_bids.mark_channels.html | 6 +- dev/generated/mne_bids.print_dir_tree.html | 6 +- dev/generated/mne_bids.read_raw_bids.html | 6 +- .../mne_bids.search_folder_for_text.html | 6 +- .../mne_bids.stats.count_events.html | 6 +- dev/generated/mne_bids.template_to_head.html | 6 +- .../mne_bids.update_anat_landmarks.html | 6 +- .../mne_bids.update_sidecar_json.html | 6 +- dev/generated/mne_bids.write_anat.html | 6 +- .../mne_bids.write_meg_calibration.html | 6 +- .../mne_bids.write_meg_crosstalk.html | 6 +- dev/generated/mne_bids.write_raw_bids.html | 6 +- dev/genindex.html | 6 +- dev/index.html | 6 +- dev/install.html | 6 +- dev/objects.inv | Bin 3759 -> 3759 bytes dev/py-modindex.html | 6 +- dev/search.html | 6 +- dev/searchindex.js | 2 +- dev/sg_execution_times.html | 32 +++++----- dev/use.html | 6 +- dev/whats_new.html | 6 +- dev/whats_new_previous_releases.html | 6 +- 78 files changed, 332 insertions(+), 331 deletions(-) diff --git a/dev/.buildinfo b/dev/.buildinfo index 088c2198d..eba07e810 100644 --- a/dev/.buildinfo +++ b/dev/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: e6bcad15472edbff205161d3a33127f4 +config: 88be86eb1ead2c30bf7578c466dc42db tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip index fc0c7f994d7a960a3f8028f4f3b5fa5ff1e3fbd4..003544785436c917a4d34dc5020548a5cf4e6fac 100644 GIT binary patch delta 242 zcmdni%eJkTjVHjHnMH&F1lX!J@|==o`dqpBhU{Ezrcafd%RNi@nO;?HejAZ32jWMS zA5dU=Q@L4YhLI#lUBE_5KBniDo4fb_mu6zC+T3$nmmNg!exxPA#9Foa`L6_iCg!T` zo?MJm1A!9TA4D^r;b-Eh+P*HE(N`QOGW~B8qXW>W>GsWxE8+S~>l03s4@YU!fI3C$}=11Ff7s2gGNtnts2P(HSJK(gvh? Ls-|bQG5P`kUV~WI delta 242 zcmdni%eJkTjVHjHnMH&F1l*H1@|==oGD+TiLw2qVok z0}4#K$(v>zsgBP|Igx8%*weA* z3^FT9e_qnw{K>20a`J=6+~+%Pe0wv=m_HT zwJ~*D@NUnch@xj%Z;qWcpOO zId1DuFdg}Pxf)P@I};z{2VtgHmD|54GM+bJVyoJIG>9>b55$m7WZbO{V%+LsJR--$ zTD5(_YDUgXkjQEgrW|P|o~rGV22AVKfsE;=!kL_b_D<)IU~&hVJ3RtKzp0$QFoMYi zXz%pr5lpTiS}zi)4k%w7$>asJcKZHEpgddEbk-;c?H$Er1>(1Z_^ega&qgu1f%u}) MKpJRIY&25<0J=R>HUIzs delta 247 zcmZ3xopbGWPM!d7W)=|!5b#aj$fK#nB@(<4B%Zu0bn5lk*X zd#68-U~&b~dXYeNK>6ZGCNH41)AvUL<=vB~vqnK^? - Overview: module code — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation + Overview: module code — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+

MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

diff --git a/dev/_modules/mne_bids/copyfiles.html b/dev/_modules/mne_bids/copyfiles.html index 418f000fa..1a7bcb552 100644 --- a/dev/_modules/mne_bids/copyfiles.html +++ b/dev/_modules/mne_bids/copyfiles.html @@ -7,7 +7,7 @@ - mne_bids.copyfiles — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation + mne_bids.copyfiles — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+

MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

diff --git a/dev/_modules/mne_bids/dig.html b/dev/_modules/mne_bids/dig.html index f781718c3..794a82bb6 100644 --- a/dev/_modules/mne_bids/dig.html +++ b/dev/_modules/mne_bids/dig.html @@ -7,7 +7,7 @@ - mne_bids.dig — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation + mne_bids.dig — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+

MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

diff --git a/dev/_modules/mne_bids/inspect.html b/dev/_modules/mne_bids/inspect.html index bb97f6ff0..6b993acfd 100644 --- a/dev/_modules/mne_bids/inspect.html +++ b/dev/_modules/mne_bids/inspect.html @@ -7,7 +7,7 @@ - mne_bids.inspect — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation + mne_bids.inspect — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+

MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

diff --git a/dev/_modules/mne_bids/path.html b/dev/_modules/mne_bids/path.html index cfd4b2b33..54965e72d 100644 --- a/dev/_modules/mne_bids/path.html +++ b/dev/_modules/mne_bids/path.html @@ -7,7 +7,7 @@ - mne_bids.path — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation + mne_bids.path — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+

MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

diff --git a/dev/_modules/mne_bids/read.html b/dev/_modules/mne_bids/read.html index 15fa807bf..683c6e1b4 100644 --- a/dev/_modules/mne_bids/read.html +++ b/dev/_modules/mne_bids/read.html @@ -7,7 +7,7 @@ - mne_bids.read — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation + mne_bids.read — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+

MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

diff --git a/dev/_modules/mne_bids/report/_report.html b/dev/_modules/mne_bids/report/_report.html index 071c35c2f..0cea84fed 100644 --- a/dev/_modules/mne_bids/report/_report.html +++ b/dev/_modules/mne_bids/report/_report.html @@ -7,7 +7,7 @@ - mne_bids.report._report — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation + mne_bids.report._report — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+

MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

diff --git a/dev/_modules/mne_bids/sidecar_updates.html b/dev/_modules/mne_bids/sidecar_updates.html index ea37d17f3..9a330ae19 100644 --- a/dev/_modules/mne_bids/sidecar_updates.html +++ b/dev/_modules/mne_bids/sidecar_updates.html @@ -7,7 +7,7 @@ - mne_bids.sidecar_updates — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation + mne_bids.sidecar_updates — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+

MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

@@ -748,7 +748,7 @@

Source code for mne_bids.sidecar_updates

 
     if bids_path_mri.suffix is None:
         raise ValueError(
-            'Please specify the "suffix" entity of the provided ' "bids_path."
+            'Please specify the "suffix" entity of the provided bids_path.'
         )
     elif bids_path_mri.suffix not in ("T1w", "FLASH"):
         raise ValueError(
diff --git a/dev/_modules/mne_bids/stats.html b/dev/_modules/mne_bids/stats.html
index b8e1b80f7..e698296fd 100644
--- a/dev/_modules/mne_bids/stats.html
+++ b/dev/_modules/mne_bids/stats.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.stats — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation
+    mne_bids.stats — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    
MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+    
MNE-BIDS 0.16.0.dev11+gdbdf957f documentation
diff --git a/dev/_modules/mne_bids/utils.html b/dev/_modules/mne_bids/utils.html index d3749db47..4e653acc0 100644 --- a/dev/_modules/mne_bids/utils.html +++ b/dev/_modules/mne_bids/utils.html @@ -7,7 +7,7 @@ - mne_bids.utils — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation + mne_bids.utils — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+

MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

@@ -740,7 +740,7 @@

Source code for mne_bids.utils

     """Write JSON to a file."""
     if op.exists(fname) and not overwrite:
         raise FileExistsError(
-            f'"{fname}" already exists. ' "Please set overwrite to True."
+            f'"{fname}" already exists. Please set overwrite to True.'
         )
 
     json_output = json.dumps(dictionary, indent=4)
@@ -756,7 +756,7 @@ 
Source code for mne_bids.utils
     """Write an ordered dictionary to a .tsv file."""
     if op.exists(fname) and not overwrite:
         raise FileExistsError(
-            f'"{fname}" already exists. ' "Please set overwrite to True."
+            f'"{fname}" already exists. Please set overwrite to True.'
         )
     _to_tsv(dictionary, fname)
 
@@ -767,7 +767,7 @@ 
Source code for mne_bids.utils
     """Write text to a file."""
     if op.exists(fname) and not overwrite:
         raise FileExistsError(
-            f'"{fname}" already exists. ' "Please set overwrite to True."
+            f'"{fname}" already exists. Please set overwrite to True.'
         )
     with open(fname, "w", encoding="utf-8-sig") as fid:
         fid.write(text)
diff --git a/dev/_modules/mne_bids/write.html b/dev/_modules/mne_bids/write.html
index 51158e12b..c870cc75e 100644
--- a/dev/_modules/mne_bids/write.html
+++ b/dev/_modules/mne_bids/write.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.write — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation
+    mne_bids.write — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    
MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+    
MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

   
 

     
@@ -1802,7 +1802,7 @@ 
Source code for mne_bids.write
 
     # Perform input checks
     if dataset_type not in ["raw", "derivative"]:
-        raise ValueError('`dataset_type` must be either "raw" or ' '"derivative."')
+        raise ValueError('`dataset_type` must be either "raw" or "derivative."')
     if isinstance(doi, str):
         if not doi.startswith("doi:"):
             warn(
@@ -1821,7 +1821,7 @@ 
Source code for mne_bids.write
         for i in generated_by:
             if "Name" not in i:
                 raise ValueError(
-                    '"Name" is a required field for each dict in ' "generated_by"
+                    '"Name" is a required field for each dict in generated_by'
                 )
             if not set(i.keys()).issubset(generated_by_keys):
                 raise ValueError(msg_key.format(i.keys() - generated_by_keys))
@@ -2355,7 +2355,7 @@ 
Source code for mne_bids.write
         del er_bids_path, er_date, er_session
     elif isinstance(empty_room, BIDSPath):
         if bids_path.datatype != "meg":
-            raise ValueError('"empty_room" is only supported for ' "MEG data.")
+            raise ValueError('"empty_room" is only supported for MEG data.')
         if data_is_emptyroom:
             raise ValueError(
                 "You cannot write empty-room data and pass "
@@ -3075,7 +3075,7 @@ 
Source code for mne_bids.write
 
     if not all(status in ["good", "bad"] for status in status):
         raise ValueError(
-            "Setting the status of a channel must only be " '"good", or "bad".'
+            'Setting the status of a channel must only be "good", or "bad".'
         )
 
     # Read sidecar and create required columns if they do not exist.
@@ -3084,7 +3084,7 @@ 
Source code for mne_bids.write
         tsv_data["status"] = ["good"] * len(tsv_data["name"])
 
     if "status_description" not in tsv_data:
-        logger.info('No "status_description" column found in input file. ' "Creating.")
+        logger.info('No "status_description" column found in input file. Creating.')
         tsv_data["status_description"] = ["n/a"] * len(tsv_data["name"])
 
     # Now actually mark the user-requested channels as bad.
diff --git a/dev/_static/documentation_options.js b/dev/_static/documentation_options.js
index f7d97be7d..683867597 100644
--- a/dev/_static/documentation_options.js
+++ b/dev/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.16.0.dev10+g4c3e7535',
+    VERSION: '0.16.0.dev11+gdbdf957f',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/dev/api.html b/dev/api.html
index 52ca1f61e..0b3a1cbdc 100644
--- a/dev/api.html
+++ b/dev/api.html
@@ -8,7 +8,7 @@
     
     
 
-    API Documentation — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation
+    API Documentation — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation
   
   
   
@@ -41,7 +41,7 @@
 
   
 
-    
+    
     
     
     
@@ -150,7 +150,7 @@
   
   
   
-    
MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+    
MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

   
 

     
diff --git a/dev/authors.html b/dev/authors.html
index 032a8115a..5cb1c6336 100644
--- a/dev/authors.html
+++ b/dev/authors.html
@@ -8,7 +8,7 @@
     
     
 
-    <no title> — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation
+    <no title> — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation
   
   
   
@@ -41,7 +41,7 @@
 
   
 
-    
+    
     
     
     
@@ -148,7 +148,7 @@
   
   
   
-    
MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+    
MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

   
 

     
diff --git a/dev/auto_examples/anonymize_dataset.html b/dev/auto_examples/anonymize_dataset.html
index 510a9cdd9..f94a3da75 100644
--- a/dev/auto_examples/anonymize_dataset.html
+++ b/dev/auto_examples/anonymize_dataset.html
@@ -8,7 +8,7 @@
     
     
 
-    13. Anonymizing a BIDS dataset — MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation
+    13. Anonymizing a BIDS dataset — MNE-BIDS 0.16.0.dev11+gdbdf957f documentation
   
   
   
@@ -41,7 +41,7 @@
 
   
 
-    
+    
     
     
     
@@ -151,7 +151,7 @@
   
   
   
-    
MNE-BIDS 0.16.0.dev10+g4c3e7535 documentation

+    
MNE-BIDS 0.16.0.dev11+gdbdf957f documentation

   
 

     
@@ -675,7 +675,7 @@ 
Basic anonymizationSpecifying subject IDsSpecifying subject IDsSpecifying subject IDs

 

 
@@ -930,9 +930,9 @@ 
ReproducibilityTotal running time of the script: (0 minutes 11.228 seconds)

+
Total running time of the script: (0 minutes 11.205 seconds)

 
     
@@ -1127,7 +1127,7 @@ 
Cite mne-bidshttps://bids-standard.github.io/bids-validator/

 
Command line tool: https://www.npmjs.com/package/bids-validator

-
Total running time of the script: (0 minutes 0.346 seconds)

+
Total running time of the script: (0 minutes 0.352 seconds)
-

Total running time of the script: (0 minutes 1.878 seconds)

+

Total running time of the script: (0 minutes 1.872 seconds)

-

Total running time of the script: (0 minutes 1.235 seconds)

+

Total running time of the script: (0 minutes 1.270 seconds)

This should be very similar to the ds000248 dataset_description.json!

-

Total running time of the script: (0 minutes 3.663 seconds)

+

Total running time of the script: (0 minutes 3.683 seconds)

-

Total running time of the script: (0 minutes 12.786 seconds)

+

Total running time of the script: (0 minutes 12.254 seconds)