INFRA: Drop numeric XX- from markdown file names

.circleci/config.yml

@@ -73,7 +73,9 @@ jobs:
       - run:
           name: install dependencies
           command: |
-            apt-get update && apt install -y python3-pip
+            apt-get update && apt install -y python3-pip && apt install -y python3-venv
+            python3 -m venv env
+            source env/bin/activate
             python3 -m pip install --upgrade pip
             python3 -m pip install -r  ~/project/requirements.txt
             python3 -m pip install ~/project/tools/schemacode/[render]
@@ -83,6 +85,7 @@ jobs:
       - run:
           name: generate pdf version docs
           command: |
+            source env/bin/activate
             cd ~/project/pdf_build_src
             bash build_pdf.sh
             mv ~/project/pdf_build_src/bids-spec.pdf ~/project/bids-spec.pdf

CODEOWNERS

@@ -5,19 +5,15 @@
 # Request for Review) please add your GitHub username next to the file you want to
 # monitor below.
 
-# Add your GitHub name below to get notified about proposed releases
-/src/CHANGES.md @chrisgorgo @sappelhoff @CPernet
-
 # Individual sections
-/src/01-common-principles.md @chrisgorgo @DimitriPapadopoulos
-/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @chrisgorgo
-/src/04-modality-specific-files/03-electroencephalography.md @sappelhoff @ezemikulan
-/src/04-modality-specific-files/04-intracranial-electroencephalography.md @ezemikulan
-/src/05-derivatives/03-imaging.md @effigies
-/src/05-derivatives/04-structural-derivatives.md @edickie @ahoopes
-/src/05-derivatives/05-functional-derivatives.md @effigies
-/src/05-derivatives/06-diffusion-derivatives.md @francopestilli @oesteban @Lestropie
-/src/appendices/meg-file-formats.md @monkeyman192
+/src/common-principles.md @chrisgorgo @DimitriPapadopoulos
+/src/modality-specific-files/magnetic-resonance-imaging-data.md @chrisgorgo
+/src/modality-specific-files/electroencephalography.md @sappelhoff @ezemikulan
+/src/modality-specific-files/intracranial-electroencephalography.md @ezemikulan
+/src/derivatives/imaging.md @effigies
+/src/derivatives/structural-derivatives.md @edickie @ahoopes
+/src/derivatives/functional-derivatives.md @effigies
+/src/derivatives/diffusion-derivatives.md @francopestilli @oesteban @Lestropie
 
 # The schema
 /src/schema/ @tsalo @erdalkaraca

mkdocs.yml

@@ -1,5 +1,48 @@
 site_name: Brain Imaging Data Structure v1.7.1-dev
 site_url: https://bids-specification.readthedocs.io/en/stable/
+nav:
+    - The BIDS Specification:
+      - Introduction: introduction.md
+      - Common principles: common-principles.md
+      - Modality agnostic files: modality-agnostic-files.md
+      - Modality specific files:
+        - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md
+        - Magnetoencephalography: modality-specific-files/magnetoencephalography.md
+        - Electroencephalography: modality-specific-files/electroencephalography.md
+        - Intracranial Electroencephalography: modality-specific-files/intracranial-electroencephalography.md
+        - Task events: modality-specific-files/task-events.md
+        - Physiological and other continuous recordings: modality-specific-files/physiological-and-other-continuous-recordings.md
+        - Behavioral experiments (with no neural recordings): modality-specific-files/behavioral-experiments.md
+        - Genetic Descriptor: modality-specific-files/genetic-descriptor.md
+        - Positron Emission Tomography: modality-specific-files/positron-emission-tomography.md
+        - Microscopy: modality-specific-files/microscopy.md
+        - Near-Infrared Spectroscopy: modality-specific-files/near-infrared-spectroscopy.md
+      - Derivatives:
+        - BIDS Derivatives: derivatives/introduction.md
+        - Common data types and metadata: derivatives/common-data-types.md
+        - Imaging data types: derivatives/imaging.md
+      - Longitudinal and multi-site studies: longitudinal-and-multi-site-studies.md
+      - Glossary: glossary.md
+      - BIDS Extension Proposals: extensions.md
+      - Appendix:
+        - Contributors: appendices/contributors.md
+        - Licenses: appendices/licenses.md
+        - Entity table: appendices/entity-table.md
+        - Entities: appendices/entities.md
+        - File collections: appendices/file-collections.md
+        - Units: appendices/units.md
+        - Hierarchical Event Descriptors: appendices/hed.md
+        - MEG file formats: appendices/meg-file-formats.md
+        - MEG systems: appendices/meg-systems.md
+        - Coordinate systems: appendices/coordinate-systems.md
+        - Quantitative MRI: appendices/qmri.md
+        - Arterial Spin Labeling: appendices/arterial-spin-labeling.md
+        - Cross modality correspondence: appendices/cross-modality-correspondence.md
+      - Changelog: CHANGES.md
+    - The BIDS Starter Kit:
+      - Website: https://bids-standard.github.io/bids-starter-kit
+      - Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html
+      - GitHub repository: https://github.com/bids-standard/bids-starter-kit
 theme:
     name: material
     favicon: images/favicon.png
@@ -33,6 +76,25 @@ plugins:
         module_name: tools/mkdocs_macros_bids/main
     - redirects:
         redirect_maps:
+            '01-introduction.md': 'introduction.md'
+            '02-common-principles.md': 'common-principles.md'
+            '03-modality-agnostic-files.md': 'modality-agnostic-files.md'
+            '04-modality-specific-files/01-magnetic-resonance-imaging-data.md': 'modality-specific-files/magnetic-resonance-imaging-data.md'
+            '04-modality-specific-files/02-magnetoencephalography.md': 'modality-specific-files/magnetoencephalography.md'
+            '04-modality-specific-files/03-electroencephalography.md': 'modality-specific-files/electroencephalography.md'
+            '04-modality-specific-files/04-intracranial-electroencephalography.md': 'modality-specific-files/intracranial-electroencephalography.md'
+            '04-modality-specific-files/05-task-events.md': 'modality-specific-files/task-events.md'
+            '04-modality-specific-files/06-physiological-and-other-continuous-recordings.md': 'modality-specific-files/physiological-and-other-continuous-recordings.md'
+            '04-modality-specific-files/07-behavioral-experiments.md': 'modality-specific-files/behavioral-experiments.md'
+            '04-modality-specific-files/08-genetic-descriptor.md': 'modality-specific-files/genetic-descriptor.md'
+            '04-modality-specific-files/09-positron-emission-tomography.md': 'modality-specific-files/positron-emission-tomography.md'
+            '04-modality-specific-files/10-microscopy.md': 'modality-specific-files/microscopy.md'
+            '04-modality-specific-files/11-near-infrared-spectroscopy.md': 'modality-specific-files/near-infrared-spectroscopy.md'
+            '05-derivatives/01-introduction.md': 'derivatives/introduction.md'
+            '05-derivatives/02-common-data-types.md': 'derivatives/common-data-types.md'
+            '05-derivatives/03-imaging.md': 'derivatives/imaging.md'
+            '06-longitudinal-and-multi-site-studies.md': 'longitudinal-and-multi-site-studies.md'
+            '07-extensions.md': 'extensions.md'
             '99-appendices/14-glossary.md': 'glossary.md'
             '99-appendices/01-contributors.md': 'appendices/contributors.md'
             '99-appendices/02-licenses.md': 'appendices/licenses.md'
@@ -49,46 +111,3 @@ plugins:
             '99-appendices/13-cross-modality-correspondence.md': 'appendices/cross-modality-correspondence.md'
 docs_dir: 'src'
 use_directory_urls: false
-nav:
-    - The BIDS Specification:
-      - Introduction: 01-introduction.md
-      - Common principles: 02-common-principles.md
-      - Modality agnostic files: 03-modality-agnostic-files.md
-      - Modality specific files:
-        - Magnetic Resonance Imaging: 04-modality-specific-files/01-magnetic-resonance-imaging-data.md
-        - Magnetoencephalography: 04-modality-specific-files/02-magnetoencephalography.md
-        - Electroencephalography: 04-modality-specific-files/03-electroencephalography.md
-        - Intracranial Electroencephalography: 04-modality-specific-files/04-intracranial-electroencephalography.md
-        - Task events: 04-modality-specific-files/05-task-events.md
-        - Physiological and other continuous recordings: 04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
-        - Behavioral experiments (with no neural recordings): 04-modality-specific-files/07-behavioral-experiments.md
-        - Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md
-        - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md
-        - Microscopy: 04-modality-specific-files/10-microscopy.md
-        - Near-Infrared Spectroscopy: 04-modality-specific-files/11-near-infrared-spectroscopy.md
-      - Derivatives:
-        - BIDS Derivatives: 05-derivatives/01-introduction.md
-        - Common data types and metadata: 05-derivatives/02-common-data-types.md
-        - Imaging data types: 05-derivatives/03-imaging.md
-      - Longitudinal and multi-site studies: 06-longitudinal-and-multi-site-studies.md
-      - Glossary: glossary.md
-      - BIDS Extension Proposals: 07-extensions.md
-      - Appendix:
-        - Contributors: appendices/contributors.md
-        - Licenses: appendices/licenses.md
-        - Entity table: appendices/entity-table.md
-        - Entities: appendices/entities.md
-        - File collections: appendices/file-collections.md
-        - Units: appendices/units.md
-        - Hierarchical Event Descriptors: appendices/hed.md
-        - MEG file formats: appendices/meg-file-formats.md
-        - MEG systems: appendices/meg-systems.md
-        - Coordinate systems: appendices/coordinate-systems.md
-        - Quantitative MRI: appendices/qmri.md
-        - Arterial Spin Labeling: appendices/arterial-spin-labeling.md
-        - Cross modality correspondence: appendices/cross-modality-correspondence.md
-      - Changelog: CHANGES.md
-    - The BIDS Starter Kit:
-      - Website: https://bids-standard.github.io/bids-starter-kit
-      - Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html
-      - GitHub repository: https://github.com/bids-standard/bids-starter-kit

pdf_build_src/build_pdf.sh

@@ -4,20 +4,27 @@
 set -eu
 
 # prepare the copied src directory
+echo "Running: process_markdowns.py"
 python3 process_markdowns.py
 
 # copy pandoc_script into the temp src_copy directory
+echo "Running: copying files to src_copy/src"
 cp pandoc_script.py header.tex cover.tex header_setup.tex src_copy/src
 
 # run pandoc_script from src_copy directory
+echo "Running: cd to src_copy/src and run pandoc_script.py"
 pushd src_copy/src
 python3 pandoc_script.py
+
+echo "Running: Moving built spec PDF and log JSON to pdf_build_src"
 mv bids-spec.pdf ../..
 mv bids-spec_pandoc_log.json ../..
 popd
 
 # Do a check on the pandoc log file
+echo "Running: check_pandoc_log.py"
 python3 check_pandoc_log.py
 
 # delete the duplicated src directory
+echo "Running: remove unneeded src_copy directory"
 rm -rf src_copy

src/CHANGES.md

@@ -489,30 +489,30 @@
 
 -   Added support for MEG data (merged BEP008).
 -   Added `SequenceName` field.
--   Added support for describing events with Hierarchical Event Descriptors: [4.3 Task events](04-modality-specific-files/05-task-events.md).
--   Added `VolumeTiming` and `AcquisitionDuration` fields: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for describing events with Hierarchical Event Descriptors: [4.3 Task events](modality-specific-files/task-events.md).
+-   Added `VolumeTiming` and `AcquisitionDuration` fields: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 -   Added `DwellTime` field.
 
 ## [1.0.2](https://doi.org/10.5281/zenodo.3759801) (2017-07-18)
 
--   Added support for high resolution (anatomical) T2star images: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added support for multiple defacing masks: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added optional key and metadata field for contrast enhanced structural scans: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added `DelayTime` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added support for multi echo BOLD data: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for high resolution (anatomical) T2star images: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added support for multiple defacing masks: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added optional key and metadata field for contrast enhanced structural scans: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added `DelayTime` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for multi echo BOLD data: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 
 ## [1.0.1](https://doi.org/10.5281/zenodo.3759788) (2017-03-13)
 
--   Added `InstitutionName` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `InstitutionAddress` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `DeviceSerialNumber` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `TotalReadoutTime to` functional images metadata list: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `InstitutionName` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `InstitutionAddress` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `DeviceSerialNumber` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `TotalReadoutTime to` functional images metadata list: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 
 ## 1.0.1-rc1
 
--   Added T1 Rho maps: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added support for phenotypic information split into multiple files: [3.2 Participant key file](03-modality-agnostic-files.md#participants-file).
+-   Added T1 Rho maps: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added support for phenotypic information split into multiple files: [3.2 Participant key file](modality-agnostic-files.md#participants-file).
 -   Added recommendations for multi site datasets.
 -   Added `SoftwareVersions`.
 -   Added `run-<run_index>` to the phase encoding maps. Improved the description.

src/appendices/arterial-spin-labeling.md

@@ -73,7 +73,7 @@ Y. Suzuki and [OSIPI Task force 4.1: ASL lexicon milestone 1](https://osipi.gith
 
 ### (P)CASL sequence
 
-![PCASL](../04-modality-specific-files/images/asl_pcasl_sequence.png)
+![PCASL](../modality-specific-files/images/asl_pcasl_sequence.png)
 
 For (P)CASL, specifying the `LabelingDuration` and the `PostLabelingDelay` is required.
 The `LabelingDuration` is defined as the total duration of the labeling pulse train in seconds.
@@ -89,7 +89,7 @@ whereas in case of `CASL`,the recommended `CASLType` field describes if a separa
 
 ### (P)CASL Labeling Pulses
 
-![PCASL Labeling Pulses](../04-modality-specific-files/images/asl_pcasl_labeling_pulses.png)
+![PCASL Labeling Pulses](../modality-specific-files/images/asl_pcasl_labeling_pulses.png)
 
 Several recommended metadata fields describe the labeling pulses of the labeling pulse train in PCASL.
 The `LabelingPulseAverageGradient` and the `LabelingPulseMaximumGradient` are the average labeling gradient
@@ -101,23 +101,23 @@ and the delay between the peaks of the individual labeling pulses in millisecond
 
 ### PASL sequence
 
-![PASL without Bolus Cut-off](../04-modality-specific-files/images/asl_pasl_boluscutoff_false.png)
+![PASL without Bolus Cut-off](../modality-specific-files/images/asl_pasl_boluscutoff_false.png)
 
 For PASL, specifying the `PostLabelingDelay` is required.
 `PostLabelingDelay` is the time, in seconds, from the middle of the labeling pulse until the middle of
 the excitation pulse applied to the imaging slab (for 3D acquisition) or first slice (for 2D acquisition).
 Additionally, the `BolusCutOffFlag` field is required,
 which is a boolean indicating if a bolus cut-off technique has been applied.
 
-![PASL QUIPSSII](../04-modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png)
+![PASL QUIPSSII](../modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png)
 
 When `BolusCutOffFlag` is set true for `PASL`, two additional metadata fields are required:
 `BolusCutOffTechnique` and `BolusCutOffDelay`.
 In this example, the `BolusCutOffTechnique`, which is the name of the technique used for applying a bolus cut-off,
 is QUIPSS-II consisting of only one bolus cut-off pulse.
 The `BolusCutOffDelay` is therefore a number, representing the duration between the end of the labeling and the start of the bolus cut-off saturation pulse, in seconds.
 
-![PASL Q2TIPS](../04-modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png)
+![PASL Q2TIPS](../modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png)
 
 In this example, the `BolusCutOffTechnique` applied is Q2TIPS, consisting of multiple bolus cut-off pulses.
 In this case, only the duration of the first and last pulse should be specified in `BolusCutOffDelay`.
@@ -127,4 +127,4 @@ In this case, only the duration of the first and last pulse should be specified
 The specification includes a dependency table, describing metadata field dependencies for ASL.
 This flowchart is intended to further clarify that table.
 
-![ASL Flowchart](../04-modality-specific-files/images/asl_flowchart.png)
+![ASL Flowchart](../modality-specific-files/images/asl_flowchart.png)