Merge pull request #1794 from bids-standard/tsv-fences

[ENH] Render code blocks with language "tsv" as tables

.pre-commit-config.yaml

@@ -10,6 +10,7 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
+        args: [--unsafe]
       - id: check-json
       - id: check-toml
       - id: check-ast

mkdocs.yml

@@ -104,7 +104,12 @@ extra_javascript:
 markdown_extensions:
   - toc:
       anchorlink: true
-  - pymdownx.superfences
+  - pymdownx.superfences:
+      preserve_tabs: true
+      custom_fences:
+        - name: tsv
+          class: tsv
+          format: !!python/name:bidsschematools.render.tsv.fence
   - admonition
   - pymdownx.details
 plugins:

pdf_build_src/pandoc_script.py

@@ -39,7 +39,7 @@ def _flatten_values(lst):
     fname_mkdocs_yml = _find(HERE, "mkdocs.yml")
 
     with open(fname_mkdocs_yml, "r") as stream:
-        mkdocs_yml = yaml.safe_load(stream)
+        mkdocs_yml = yaml.load(stream, yaml.Loader)
 
     sections = mkdocs_yml["nav"][0]["The BIDS Specification"]
 

src/appendices/arterial-spin-labeling.md

@@ -26,7 +26,7 @@ and the exact volume_type series should be specified in the `*_aslcontext.tsv`.
 
 Example of `*_aslcontext.tsv`:
 
-```Text
+```tsv
 volume_type
 control
 label
@@ -44,7 +44,7 @@ In this case, the `deltam` should be included in the `*_asl.nii[.gz]` and specif
 
 Example of `*_aslcontext.tsv`:
 
-```Text
+```tsv
 volume_type
 deltam
 m0scan
@@ -58,7 +58,7 @@ the `cbf` should be included in the `*_asl.nii[.gz]` and specified in the `*_asl
 
 Example of `*_aslcontext.tsv`:
 
-```Text
+```tsv
 volume_type
 cbf
 m0scan

src/appendices/hed.md

@@ -44,10 +44,10 @@ meanings in associated JSON sidecar files (`events.json`).
 (`trial_type`, `response_time`, and `stim_file`) in addition to
 the required `onset` and `duration` columns.
 
-```Text
-onset  duration  trial_type  response_time stim_file
-1.2    0.6       go          1.435         images/red_square.jpg
-5.6    0.6       stop        n/a           images/blue_square.jpg
+```tsv
+onset	duration	trial_type	response_time	stim_file
+1.2	0.6	go	1.435	images/red_square.jpg
+5.6	0.6	stop	n/a	images/blue_square.jpg
 ```
 
 The `trial_type` column in the above example contains a limited number of distinct

src/derivatives/common-data-types.md

@@ -328,11 +328,12 @@ A guide for using macros can be found at
 
 Contents of the `descriptions.tsv` file:
 
-| desc_id | description                                                                                     |
-| ------- | ----------------------------------------------------------------------------------------------- |
-| Filt    | low-pass filtered at 30Hz                                                                       |
-| FiltDs  | low-pass filtered at 30Hz, downsampled to 250Hz                                                 |
-| preproc | low-pass filtered at 30Hz, downsampled to 250Hz, and rereferenced to a common average reference |
+```tsv
+desc_id	description
+Filt	low-pass filtered at 30Hz
+FiltDs	low-pass filtered at 30Hz, downsampled to 250Hz
+preproc	low-pass filtered at 30Hz, downsampled to 250Hz, and rereferenced to a common average reference
+```
 
 <!-- Link Definitions -->
 

src/longitudinal-and-multi-site-studies.md

@@ -65,7 +65,7 @@ A guide for using macros can be found at
 
 `sub-control01_sessions.tsv` content:
 
-```Text
+```tsv
 session_id	acq_time	systolic_blood_pressure
 ses-predrug	2009-06-15T13:45:30	120
 ses-postdrug	2009-06-16T13:45:30	100

src/modality-agnostic-files.md

@@ -246,11 +246,11 @@ available").
 
 `participants.tsv` example:
 
-```Text
-participant_id age sex handedness group
-sub-01 34 M right read
-sub-02 12 F right write
-sub-03 33 F n/a read
+```tsv
+participant_id	age	sex	handedness	group
+sub-01	34	M	right	read
+sub-02	12	F	right	write
+sub-03	33	F	n/a	read
 ```
 
 It is RECOMMENDED to accompany each `participants.tsv` file with a sidecar
@@ -320,13 +320,13 @@ and a guide for using macros can be found at
 
 `samples.tsv` example:
 
-```Text
-sample_id participant_id sample_type derived_from
-sample-01 sub-01 tissue n/a
-sample-02 sub-01 tissue sample-01
-sample-03 sub-01 tissue sample-01
-sample-04 sub-02 tissue n/a
-sample-05 sub-02 tissue n/a
+```tsv
+sample_id	participant_id	sample_type	derived_from
+sample-01	sub-01	tissue	n/a
+sample-02	sub-01	tissue	sample-01
+sample-03	sub-01	tissue	sample-01
+sample-04	sub-02	tissue	n/a
+sample-05	sub-02	tissue	n/a
 ```
 
 It is RECOMMENDED to accompany each `samples.tsv` file with a sidecar
@@ -486,7 +486,7 @@ All such included additional fields SHOULD be documented in an accompanying
 
 Example `_scans.tsv`:
 
-```Text
+```tsv
 filename	acq_time
 func/sub-control01_task-nback_bold.nii.gz	1877-06-15T13:45:30
 func/sub-control01_task-motor_bold.nii.gz	1877-06-15T13:55:33
@@ -522,7 +522,7 @@ and a guide for using macros can be found at
 
 `_sessions.tsv` example:
 
-```Text
+```tsv
 session_id	acq_time	systolic_blood_pressure
 ses-predrug	2009-06-15T13:45:30	120
 ses-postdrug	2009-06-16T13:45:30	100

src/modality-specific-files/behavioral-experiments.md

@@ -78,7 +78,7 @@ A guide for using macros can be found at
 
 ## Example `_beh.tsv`
 
-```Text
+```tsv
 trial	response	response_time	stim_file
 congruent	red	1.435	images/word-red_color-red.jpg
 incongruent	red	1.739	images/word-red_color-blue.jpg

src/modality-specific-files/electroencephalography.md

@@ -274,12 +274,12 @@ Examples of free-form text for field `description`
 
 See also the corresponding [`electrodes.tsv` example](#example-_electrodestsv).
 
-```Text
-name     type  units  description                     reference     status  status_description
-VEOG     VEOG  uV     left eye                        VEOG-, VEOG+  good    n/a
-FDI      EMG   uV     left first dorsal interosseous  FDI-, FDI+    good    n/a
-Cz       EEG   uV     n/a                             REF           bad     high frequency noise
-UADC001  MISC  n/a    envelope of audio signal        n/a           good    n/a
+```tsv
+name	type	units	description	reference	status	status_description
+VEOG	VEOG	uV	left eye	VEOG-, VEOG+	good	n/a
+FDI	EMG	uV	left first dorsal interosseous	FDI-, FDI+	good	n/a
+Cz	EEG	uV	n/a	REF	bad	high frequency noise
+UADC001	MISC	n/a	envelope of audio signal	n/a	good	n/a
 ```
 
 ## Electrodes description (`*_electrodes.tsv`)
@@ -318,15 +318,15 @@ If electrodes are repositioned, it is RECOMMENDED to use multiple sessions to in
 
 See also the corresponding [`channels.tsv` example](#example-_channelstsv).
 
-```Text
-name   x        y	       z        type     material
-VEOG+  n/a      n/a      n/a      cup      Ag/AgCl
-VEOG-  n/a      n/a      n/a      cup      Ag/AgCl
-FDI+   n/a      n/a      n/a      cup      Ag/AgCl
-FDI-   n/a      n/a      n/a      cup      Ag/AgCl
-GND    -0.0707  0.0000   -0.0707  clip-on  Ag/AgCl
-Cz     0.0000   0.0714   0.0699   cup      Ag/AgCl
-REF    -0.0742  -0.0200  -0.0100  cup      Ag/AgCl
+```tsv
+name	x	y	z	type	material
+VEOG+	n/a	n/a	n/a	cup	Ag/AgCl
+VEOG-	n/a	n/a	n/a	cup	Ag/AgCl
+FDI+	n/a	n/a	n/a	cup	Ag/AgCl
+FDI-	n/a	n/a	n/a	cup	Ag/AgCl
+GND	-0.0707	0.0000	-0.0707	clip-on	Ag/AgCl
+Cz	0.0000	0.0714	0.0699	cup	Ag/AgCl
+REF	-0.0742	-0.0200	-0.0100	cup	Ag/AgCl
 ```
 
 The [`acq-<label>`](../appendices/entities.md#acq) entity can be used to

src/modality-specific-files/genetic-descriptor.md

@@ -70,7 +70,7 @@ Note that optional columns MUST be further described in an accompanying
 
 `participants.tsv` example:
 
-```Text
+```tsv
 participant_id	age	sex	group	genetic_id	idh_mutation
 sub-control01	34	M	control	124587	yes
 sub-control02	12	F	control	548936	yes

src/modality-specific-files/intracranial-electroencephalography.md

@@ -276,13 +276,13 @@ Examples of free-form text for field `description`:
 
 ### Example `*_channels.tsv`
 
-```Text
-name  type  units low_cutoff  high_cutoff status  status_description
-LT01  ECOG  uV    300         0.11        good    n/a
-LT02  ECOG  uV    300         0.11        bad     broken
-H01   SEEG  uV    300         0.11        bad     line_noise
-ECG1  ECG   uV    n/a         0.11        good    n/a
-TR1   TRIG  n/a   n/a         n/a         good    n/a
+```tsv
+name	type	units	low_cutoff	high_cutoff	status	status_description
+LT01	ECOG	uV	300	0.11	good	n/a
+LT02	ECOG	uV	300	0.11	bad	broken
+H01	SEEG	uV	300	0.11	bad	line_noise
+ECG1	ECG	uV	n/a	0.11	good	n/a
+TR1	TRIG	n/a	n/a	n/a	good	n/a
 ```
 
 ## Electrode description (`*_electrodes.tsv`)
@@ -358,11 +358,11 @@ If electrodes are repositioned, it is RECOMMENDED to use multiple sessions to in
 
 ### Example `*_electrodes.tsv`
 
-```Text
-name  x   y    z    size   manufacturer
-LT01  19  -39  -16  2.3    Integra
-LT02  23  -40  -19  2.3    Integra
-H01   27  -42  -21  5      AdTech
+```tsv
+name	x	y	z	size	manufacturer
+LT01	19	-39	-16	2.3	Integra
+LT02	23	-40	-19	2.3	Integra
+H01	27	-42	-21	5	AdTech
 ```
 
 ## Coordinate System JSON (`*_coordsystem.json`)
@@ -534,13 +534,13 @@ For example: `/stimuli/electrical_stimulation_functions/biphasic.tsv`
 
 ### Example `*_events.tsv`
 
-```Text
-onset duration trial_type             electrical_stimulation_type electrical_stimulation_site electrical_stimulation_current
-1.2   0.001    electrical_stimulation biphasic                    LT01-LT02                   0.005
-1.3   0.001    electrical_stimulation biphasic                    LT01-LT02                   0.005
-2.2   0.001    electrical_stimulation biphasic                    LT02-LT03                   0.005
-4.2   1        electrical_stimulation complex                     LT02-LT03                   n/a
-15.2  3        auditory_stimulus      n/a                         n/a                         n/a
+```tsv
+onset	duration	trial_type	electrical_stimulation_type	electrical_stimulation_site	electrical_stimulation_current
+1.2	0.001	electrical_stimulation	biphasic	LT01-LT02	0.005
+1.3	0.001	electrical_stimulation	biphasic	LT01-LT02	0.005
+2.2	0.001	electrical_stimulation	biphasic	LT02-LT03	0.005
+4.2	1	electrical_stimulation	complex	LT02-LT03	n/a
+15.2	3	auditory_stimulus	n/a	n/a	n/a
 ```
 
 <!-- Link Definitions -->

src/modality-specific-files/magnetoencephalography.md

@@ -311,12 +311,12 @@ Examples of free text for field `description`:
 
 ### Example `*_channels.tsv`
 
-```Text
-name type units description
-VEOG VEOG V vertical EOG
-FDI EMG V left first dorsal interosseous
-UDIO001 TRIG V analog trigger signal
-UADC001 AUDIO V envelope of audio signal presented to participant
+```tsv
+name	type	units	description
+VEOG	VEOG	V	vertical EOG
+FDI	EMG	V	left first dorsal interosseous
+UDIO001	TRIG	V	analog trigger signal
+UADC001	AUDIO	V	envelope of audio signal presented to participant
 ```
 
 ## Coordinate System JSON (`*_coordsystem.json`)

src/modality-specific-files/motion.md

@@ -185,21 +185,21 @@ Note that upper-case is REQUIRED:
 
 ### Example `*_channels.tsv`
 
-```Text
-name        component   type   tracked_point   units    reference_frame
-t1_acc_x    x           ACCEL  LeftFoot        m/s^2    global
-t1_acc_y    y           ACCEL  LeftFoot        m/s^2    global
-t1_acc_z    z           ACCEL  LeftFoot        m/s^2    global
-t1_gyro_x   x           GYRO   LeftFoot        rad/s    global
-t1_gyro_y   y           GYRO   LeftFoot        rad/s    global
-t1_gyro_z   z           GYRO   LeftFoot        rad/s    global
+```tsv
+name	component	type	tracked_point	units	reference_frame
+t1_acc_x	x	ACCEL	LeftFoot	m/s^2	global
+t1_acc_y	y	ACCEL	LeftFoot	m/s^2	global
+t1_acc_z	z	ACCEL	LeftFoot	m/s^2	global
+t1_gyro_x	x	GYRO	LeftFoot	rad/s	global
+t1_gyro_y	y	GYRO	LeftFoot	rad/s	global
+t1_gyro_z	z	GYRO	LeftFoot	rad/s	global
 …
-t2_acc_x    x           ACCEL  RightWrist      m/s^2    global
-t2_acc_y    y           ACCEL  RightWrist      m/s^2    global
-t2_acc_z    z           ACCEL  RightWrist      m/s^2    global
-t2_gyro_x   x           GYRO   RightWrist      rad/s    global
-t2_gyro_y   y           GYRO   RightWrist      rad/s    global
-t2_gyro_z   z           GYRO   RightWrist      rad/s    global
+t2_acc_x	x	ACCEL	RightWrist	m/s^2	global
+t2_acc_y	y	ACCEL	RightWrist	m/s^2	global
+t2_acc_z	z	ACCEL	RightWrist	m/s^2	global
+t2_gyro_x	x	GYRO	RightWrist	rad/s	global
+t2_gyro_y	y	GYRO	RightWrist	rad/s	global
+t2_gyro_z	z	GYRO	RightWrist	rad/s	global
 ```
 
 ## Reference frame description (`*_channels.json`)

src/modality-specific-files/near-infrared-spectroscopy.md

@@ -293,13 +293,13 @@ Note that upper-case is REQUIRED.
 
 ### Example `*_channels.tsv`
 
-```Text
-Name         type                   source      detector      wavelength_nominal   units
-S1-D1        NIRSCWAMPLITUDE        A1          Fz            760                  V
-S1-D1        NIRSCWAMPLITUDE        A1          Fz            850                  V
-S1-D2        NIRSCWAMPLITUDE        A1          Cz            760                  V
-S2-D1        NIRSCWAMPLITUDE        A2          Fz            760                  V
-S3-D4        NIRSCWAMPLITUDE        VisS2       VisD4         760                  V
+```tsv
+Name	type	source	detector	wavelength_nominal	units
+S1-D1	NIRSCWAMPLITUDE	A1	Fz	760	V
+S1-D1	NIRSCWAMPLITUDE	A1	Fz	850	V
+S1-D2	NIRSCWAMPLITUDE	A1	Cz	760	V
+S2-D1	NIRSCWAMPLITUDE	A2	Fz	760	V
+S3-D4	NIRSCWAMPLITUDE	VisS2	VisD4	760	V
 ```
 
 ## Optode description (`*_optodes.tsv`)
@@ -337,14 +337,14 @@ The columns of the optodes description table stored in `*_optodes.tsv` are:
 
 ### Example `*_optodes.tsv`
 
-```Text
-name    type         x          y         z          template_x    template_y   template_z
-A1      source       -0.0707    0.0000    -0.0707    -0.07         0.00         0.07
-Fz      detector     0.0000     0.0714    0.0699     0.0           0.07         0.07
-S1      source       -0.2707    0.0200    -0.1707    -0.03         0.02         -0.2
-D2      detector     0.0022     0.1214    0.0299     0.0           0.12         0.03
-VisS2   source       -0.1707    0.1200    -0.3707    -0.1          0.1          -0.4
-VisD4   detector     0.0322     0.2214    0.2299     0.02          0.22         0.23
+```tsv
+name	type	x	y	z	template_x	template_y	template_z
+A1	source	-0.0707	0.0000	-0.0707	-0.07	0.00	0.07
+Fz	detector	0.0000	0.0714	0.0699	0.0	0.07	0.07
+S1	source	-0.2707	0.0200	-0.1707	-0.03	0.02	-0.2
+D2	detector	0.0022	0.1214	0.0299	0.0	0.12	0.03
+VisS2	source	-0.1707	0.1200	-0.3707	-0.1	0.1	-0.4
+VisD4	detector	0.0322	0.2214	0.2299	0.02	0.22	0.23
 ```
 
 ## Coordinate System JSON (`*_coordsystem.json`)

src/modality-specific-files/physiological-recordings.md

@@ -94,10 +94,10 @@ A guide for using macros can be found at
 
 (after decompression)
 
-```Text
-34    110    0
-44    112    0
-23    100    1
+```tsv
+34	110	0
+44	112	0
+23	100	1
 ```
 
 Example `*_physio.json`: