[MISC] Reorder appendices

.github/pull_request_template.md

@@ -5,7 +5,7 @@ See the [CONTRIBUTING](https://github.com/bids-standard/bids-specification/blob/
 - Please keep the title of your Pull Request (PR) short but informative - it will
   appear in the changelog.
 - If you do **not** want a PR to appear in the changelog, it must receive the `exclude-from-changelog` label.
-- Please ensure your name is credited on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/99-appendices/01-contributors.md).
+- Please ensure your name is credited on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
   To add your name, please edit our [Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Contributors) and add your name with the type of contribution.
   For assistance, please tag @bids-standard/maintainers.
 - Use one of the following prefixes in the title of your PR:

CODEOWNERS

@@ -17,7 +17,7 @@
 /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/99-appendices/06-meg-file-formats.md @monkeyman192
+/src/appendices/meg-file-formats.md @monkeyman192
 
 # The schema
 /src/schema/ @tsalo @erdalkaraca

CONTRIBUTING.md

@@ -708,11 +708,11 @@ BIDS follows the
 specification, so we welcome and recognize all contributions from documentation
 to testing to code development.
 You can see a list of current contributors in the
-[BIDS specification](https://github.com/bids-standard/bids-specification/blob/master/src/99-appendices/01-contributors.md).
+[BIDS specification](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
 
 If you have made any type of contributions to the BIDS specifications, you can
 either make a change to the
-[contributors document](./src/99-appendices/01-contributors.md) and commit as
+[contributors document](./src/appendices/contributors.md) and commit as
 part of a pull request or you can edit this
 [page](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors)
 of the specification WIKI.

DECISION-MAKING.md

@@ -61,7 +61,7 @@ Leaders of BIDS Extension Proposals are listed in the
 
 ### Contributors Group
 
-Contributors are listed in [Appendix I](https://bids-specification.readthedocs.io/en/stable/99-appendices/01-contributors.html)
+Contributors are listed in the [Contributors appendix](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html)
 of the BIDS specification. Contributors who have not yet entered their name
 into this list are encouraged to edit the [Contributors WIKI page](https://github.com/bids-standard/bids-specification/wiki/Contributors)
 with their name, using the emojis listed in the WIKI to indicate their

README.md

@@ -50,7 +50,7 @@ The specification is provided in the form of a webpage, built using
 BIDS is a community-driven standard, and it depends on contributions from its members.
 We welcome new contributors, and we appreciate all contributions to the project!
 
-For a current list of our contributors, please see our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/99-appendices/01-contributors.md).
+For a current list of our contributors, please see our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
 
 When you're ready to get started, check out [our contributing guidelines](https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md).
 

Release_Protocol.md

@@ -66,7 +66,7 @@ Additionally, implement the same change in the version name perform above in the
 
 Note: this will make our continuous integration ([CircleCI](https://circleci.com/)) fail. This fails because the URL of the new ReadTheDocs rendering has not been generated at this time. It will be generated once the GitHub release has been completed.
 
-Synchronize the [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/99-appendices/01-contributors.md)
+Synchronize the [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md)
 with the [Contributors wiki page](https://github.com/bids-standard/bids-specification/wiki/Contributors)
 to ensure all contributors are duly credited.
 Be sure not to remove credits if both have been edited.
@@ -92,7 +92,7 @@ By pushing `rel/` branches to the main repository, the chances of continuous int
 discrepancies is reduced.
 
 ```Shell
-$ git add src/CHANGES.md mkdocs.yml src/99-appendices/01-contributors.md
+$ git add src/CHANGES.md mkdocs.yml src/appendices/contributors.md
 $ git commit -m 'REL: v1.2.0'
 $ git push -u upstream rel/1.2.0
 ```

mkdocs.yml

@@ -31,6 +31,22 @@ plugins:
              - css/watermark.css
     - macros:
         module_name: tools/mkdocs_macros_bids/main
+    - redirects:
+        redirect_maps:
+            '99-appendices/14-glossary.md': 'glossary.md'
+            '99-appendices/01-contributors.md': 'appendices/contributors.md'
+            '99-appendices/02-licenses.md': 'appendices/licenses.md'
+            '99-appendices/03-hed.md': 'appendices/hed.md'
+            '99-appendices/04-entity-table.md': 'appendices/entity-table.md'
+            '99-appendices/05-units.md': 'appendices/units.md'
+            '99-appendices/06-meg-file-formats.md': 'appendices/meg-file-formats.md'
+            '99-appendices/07-meg-systems.md': 'appendices/meg-systems.md'
+            '99-appendices/08-coordinate-systems.md': 'appendices/coordinate-systems.md'
+            '99-appendices/09-entities.md': 'appendices/entities.md'
+            '99-appendices/10-file-collections.md': 'appendices/file-collections.md'
+            '99-appendices/11-qmri.md': 'appendices/qmri.md'
+            '99-appendices/12-arterial-spin-labeling.md': 'appendices/arterial-spin-labeling.md'
+            '99-appendices/13-cross-modality-correspondence.md': 'appendices/cross-modality-correspondence.md'
 docs_dir: 'src'
 use_directory_urls: false
 nav:
@@ -54,22 +70,22 @@ nav:
         - 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: 99-appendices/01-contributors.md
-        - Licenses: 99-appendices/02-licenses.md
-        - Hierarchical Event Descriptors: 99-appendices/03-hed.md
-        - Entity table: 99-appendices/04-entity-table.md
-        - Units: 99-appendices/05-units.md
-        - MEG file formats: 99-appendices/06-meg-file-formats.md
-        - MEG systems: 99-appendices/07-meg-systems.md
-        - Coordinate systems: 99-appendices/08-coordinate-systems.md
-        - Entities: 99-appendices/09-entities.md
-        - File collections: 99-appendices/10-file-collections.md
-        - Quantitative MRI: 99-appendices/11-qmri.md
-        - Arterial Spin Labeling: 99-appendices/12-arterial-spin-labeling.md
-        - Cross modality correspondence: 99-appendices/13-cross-modality-correspondence.md
-        - Glossary: 99-appendices/14-glossary.md
+        - 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

pdf_build_src/pandoc_script.py

@@ -50,11 +50,11 @@ def build_pdf(filename="bids-spec.pdf", logfile="bids-spec_pandoc_log.json"):
 
     # Resources are searched relative to the working directory, but
     # we can add additional search paths using <path>:<another path>, ...
-    # When in one of the 99-appendices/ files there is a reference to
+    # When in one of the appendices/ files there is a reference to
     # "../04-modality-specific-files/images/...", then we need to use
-    # 99-appendices/ as a resource-path so that the relative files can
+    # appendices/ as a resource-path so that the relative files can
     # be found.
-    cmd += [f'--resource-path=.:{str(root / "99-appendices")}']
+    cmd += [f'--resource-path=.:{str(root / "appendices")}']
 
     # Add input files to command
     # The filenames in `markdown_list` will ensure correct order when sorted

requirements.txt

@@ -3,5 +3,6 @@ mkdocs-material>=5.4
 pymdown-extensions>=7.0.0
 mkdocs-branchcustomization-plugin~=0.1.3
 mkdocs-macros-plugin
+mkdocs-redirects
 numpy
 tools/schemacode/[render]

src/02-common-principles.md

@@ -56,11 +56,10 @@ entity instance, may be referred to as simply an "entity".
 "Subject", "session", "sample", "task", and "run" from the list of definitions
 above are all examples of entities.
 The comprehensive list of supported entities is defined in
-[Appendix IX](99-appendices/09-entities.md);
+the [Entities Appendix](appendices/entities.md);
 further, whether each is OPTIONAL, REQUIRED, or MUST NOT be provided for
 various data files, as well as their relative ordering in a filename, are
-defined in the Entity Table in
-[Appendix IV](99-appendices/04-entity-table.md).
+defined in the [Entity Tables Appendix](appendices/entity-table.md).
 
 ## Compulsory, optional, and additional data and metadata
 
@@ -134,12 +133,12 @@ In cases where an entity and a metadata field convey similar contextual
 information, the presence of an entity should not be used as a replacement for
 the corresponding metadata field.
 For instance, in echo-planar imaging MRI, the
-[`dir-<label>`](./99-appendices/09-entities.md#dir) entity MAY be used
+[`dir-<label>`](./appendices/entities.md#dir) entity MAY be used
 to distinguish files with different phase-encoding directions,
 but the file's `PhaseEncodingDirection` MUST be specified as metadata.
 
 A summary of all entities in BIDS and the order in which they MUST be
-specified is available in the [entity table](./99-appendices/04-entity-table.md)
+specified is available in the [entity table](./appendices/entity-table.md)
 in the appendix.
 
 ### Entity-linked file collections
@@ -161,7 +160,7 @@ Provided the conditions above are satisfied,
 any suffix (such as `bold`) can identify an entity-linked file collection,
 although certain suffixes are exclusive for this purpose (for example, `MP2RAGE`).
 Use cases concerning this convention are compiled in the
-[file collections](./99-appendices/10-file-collections.md) appendix.
+[file collections](./appendices/file-collections.md) appendix.
 This convention is mainly intended for but not limited to MRI modalities.
 
 ### Case collision intolerance
@@ -805,14 +804,14 @@ In case data is expressed in SI units or SI derived units, the units MAY be
 specified in the sidecar JSON file.
 In case non-standard prefixes are added to SI or non-SI units, these
 non-standard prefixed units MUST be specified in the JSON file.
-See [Appendix V](99-appendices/05-units.md) for a list of standard units and
+See the [Units Appendix](appendices/units.md) for a list of standard units and
 prefixes.
 Note also that for the *formatting* of SI units, the [CMIXF-12](https://people.csail.mit.edu/jaffer/MIXF/CMIXF-12)
 convention for encoding units is RECOMMENDED.
 CMIXF provides a consistent system for all units and prefix symbols with only basic
 characters, avoiding symbols that can cause text encoding problems; for example the
 CMIXF formatting for "micro volts" is `uV`, "degrees Celsius" is `oC` and "Ohm" is `Ohm`.
-See [Appendix V](99-appendices/05-units.md) for more information.
+See the [Units Appendix](appendices/units.md) for more information.
 
 For additional rules, see below:
 
@@ -866,7 +865,7 @@ Describing dates and timestamps:
     Some analysis software packages (for example, MNE-Python) handle their data as `.fif`
     internally and will break if recording dates are specified prior to `1902`,
     even if the original data format is not `.fif`.
-    See [MEG-file-formats](./99-appendices/06-meg-file-formats.md#recording-dates-in-fif-files)
+    See the [MEG File Formats Appendix](./appendices/meg-file-formats.md#recording-dates-in-fif-files)
     for more information.
 
 -   Age SHOULD be given as the number of years since birth at the time of

src/03-modality-agnostic-files.md

@@ -469,7 +469,7 @@ commonly used for qMRI,
 where recordings may be linked through entities such as `echo` and `part`
 (using `.nii` or `.nii.gz` extensions).
 For another example consider the case of large files in `.fif` format that are linked through the `split` entity
-(see [Split files](./99-appendices/06-meg-file-formats.md#split-files)).
+(see [Split files](./appendices/meg-file-formats.md#split-files)).
 Such recordings MUST be documented with one row per file
 (unlike the case of multi-file file formats described above).