Merge pull request #29 from bids-standard/master

update 8/22

Release_Protocol.md

@@ -35,7 +35,7 @@ $ git fetch upstream
 $ git checkout -b rel/1.2.0 upstream/master
 ```
 
-### 2. Update the version in the changelog and mkdocs.yml
+### 2. Update the version and the contributors list
 
 Change the "Unreleased" heading in
 [src/CHANGES.md](https://github.com/bids-standard/bids-specification/blob/master/src/CHANGES.md)
@@ -57,13 +57,20 @@ If the version preceding the `-dev` is not the target version, update the versio
 In the figure below, we update `v1.2.0-dev` to `v1.2.0`.
 ![dev-to-stable](release_images/site_name_release_1.2dev-1.2.png "dev-to-stable")
 
+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)
+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.
+
 ### 3. Commit changes and push to upstream
 
 By pushing `rel/` branches to the main repository, the chances of continuous integration
 discrepancies is reduced.
 
 ```Shell
-$ git add src/CHANGES.md mkdocs.yml
+$ git add src/CHANGES.md mkdocs.yml src/99-appendices/01-contributors.md
 $ git commit -m 'REL: v1.2.0'
 $ git push -u upstream rel/1.2.0
 ```
@@ -157,6 +164,10 @@ description:
 
 Click "Publish release".
 
+Verify ReadTheDocs builds complete and publish. If needed, manually
+trigger [builds](https://readthedocs.org/projects/bids-specification/builds/)
+for `stable` and the most recent tag.
+
 ### 9. Edit the mkdocs.yml file site_name to set a new development version
 
 Please submit a PR with the title `REL: <version>-dev`.

pull_request_template.md

@@ -2,6 +2,7 @@
 
 - Please keep the title of your pull request short but informative - it will 
   appear in the changelog
+- 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). 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 contact @franklin-feingold or @sappelhoff.
 - Use one of the following prefixes in the title of your pull request:
   - `[ENH]` - enhancement of the specification that adds a new feature or 
     support for a new data type

src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

@@ -214,9 +214,9 @@ based fMRI a corresponding task events file (see below) MUST be provided
 multiband acquisitions, one MAY also save the single-band reference image as
 type `sbref` (e.g. `sub-control01_task-nback_sbref.nii.gz`).
 
-Each task has a unique label MUST only include of letters and/or numbers (other
-characters including spaces and underscores are not allowed). Those labels MUST
-be consistent across subjects and sessions.
+Each task has a unique label that MUST only consist of letters and/or numbers
+(other characters, including spaces and underscores, are not allowed).
+Those labels MUST be consistent across subjects and sessions.
 
 If more than one run of the same task has been acquired a key/value pair:
 `_run-1`, `_run-2`, `_run-3` etc. MUST be used. If only one run was acquired the

src/06-extensions.md

@@ -53,6 +53,7 @@ provides a direct link to the documentation.
 | [BEP024](https://docs.google.com/document/d/1fqnJZ18x5LJC8jiJ8yvPHUGFzNBZ6gW2kywYrUKWtuo) | Computed Tomography scan (CT)                                                                              | Hugo Boniface                                                              | This effort has stalled and looking for more contributors and experts.                                                                                                                                                                    | None.                                                                                  |
 | [BEP025](https://docs.google.com/document/d/1chZv7vAPE-ebPDxMktfI9i1OkLNR2FELIfpVYsaZPr4) | Medical Population Imaging Data structure (MIDS)                                                           | Jose Manuel Saborit Torres, Maria de la Iglesia Vayá                       | This BEP is working on the automated recognition of the DICOM sequence and writing the manuscript.                                                                                                                                        | None.                                                                                  |
 | [BEP026](https://docs.google.com/document/d/14KC1d5-Lx-7ZSMtwS7pVAAvz-2WR_uoo5FvsNirzqJw) | Microelectrode Recordings (MER)                                                                            | Greydon Gilmore                                                            | Active effort. Looking for thoughts and contributions                                                                                                                                                                                     | None.                                                                                  |
+| [BEP027](https://docs.google.com/document/d/104HLZedFtx0TaXEUwd7eyWvJUlc0CcSUtCzwjNgmGxE) | BIDS Execution                                                                                             | Chris Markiewicz and Greg Kiar                                             | Partial draft seeking community input and fleshing out of some details. Examples and tooling should be available prior to release to demonstrate viability.                                                                               | None.                                                                                  |
 
 When an extension reaches maturity it is merged into the main body of the
 specification.  Below is a table of BEPs that have been merged in the main body

src/99-appendices/04-entity-table.md

@@ -15,7 +15,7 @@ A general introduction to entities is given in the section on
 | Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `proc-<label>`        | `space-<label>` |
 | anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               |                        |                |                     |                       |                 |
 | anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               | OPTIONAL               |                |                     |                       |                 |
-| func<br>(bold sbref events)                                                                    | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     |                       |                 |
+| func<br>(bold cbv phase sbref events)                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     |                       |                 |
 | func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          | OPTIONAL       |                          | OPTIONAL      |                        |                | OPTIONAL            | OPTIONAL              |                 |
 | dwi<br>(dwi bvec bval)                                                                         | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                | OPTIONAL                 | OPTIONAL      |                        |                |                     |                       |                 |
 | fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                       |                 |

src/CHANGES.md

@@ -1,10 +1,20 @@
 Changelog
 
-## [v1.2.1](https://bids-specification.readthedocs.io/en/v1.2.1/) (2019-08-14)
+## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[MISC] Add BEP027 - BIDS Execution to BEP list [#314](https://github.com/bids-standard/bids-specification/pull/314) ([effigies](https://github.com/effigies))
+-   \[FIX] Add CBV and phase to Entity table [#312](https://github.com/bids-standard/bids-specification/pull/312) ([tsalo](https://github.com/tsalo))
+-   \[ENH] Release protocol notes [#304](https://github.com/bids-standard/bids-specification/pull/304) ([franklin-feingold](https://github.com/franklin-feingold))
+-   REL: 1.3.0-dev [#303](https://github.com/bids-standard/bids-specification/pull/303) ([franklin-feingold](https://github.com/franklin-feingold))
+-   \[INFRA] Adding contributor appendix sentence to PR template  [#299](https://github.com/bids-standard/bids-specification/pull/299) ([franklin-feingold](https://github.com/franklin-feingold))
+
+## [v1.2.1](https://github.com/bids-standard/bids-specification/tree/v1.2.1) (2019-08-14)
+
+-   Sync rel/1.2.1 to master [#302](https://github.com/bids-standard/bids-specification/pull/302) ([franklin-feingold](https://github.com/franklin-feingold))
 -   FIX: repair link in anatomical MRI table [#297](https://github.com/bids-standard/bids-specification/pull/297) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Clarify requirements in Release Protocol [#294](https://github.com/bids-standard/bids-specification/pull/294) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA+FIX] Use linkchecker (from a dedicated docker image) to check all URLs [#293](https://github.com/bids-standard/bids-specification/pull/293) ([yarikoptic](https://github.com/yarikoptic))
+-   REL: v1.2.1 [#291](https://github.com/bids-standard/bids-specification/pull/291) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Adding Contributors and updating contributions [#284](https://github.com/bids-standard/bids-specification/pull/284) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[MISC] update Code of Conduct contact [#281](https://github.com/bids-standard/bids-specification/pull/281) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Update contributing guide and README to make discussion forums easy to find [#279](https://github.com/bids-standard/bids-specification/pull/279) ([emdupre](https://github.com/emdupre))
@@ -58,7 +68,7 @@ Changelog
 -   \[FIX] Specify marker file names for KIT data (MEG) [#62](https://github.com/bids-standard/bids-specification/pull/62) ([monkeyman192](https://github.com/monkeyman192))
 -   \[FIX] Remove father-level for meg filetypes other than BTi/4D data [#19](https://github.com/bids-standard/bids-specification/pull/19) ([teonbrooks](https://github.com/teonbrooks))
 
-## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/) (2019-03-04)
+## [v1.2.0](https://github.com/bids-standard/bids-specification/tree/v1.2.0) (2019-03-04)
 
 -   REL: v1.2.0 [#161](https://github.com/bids-standard/bids-specification/pull/161) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Adding Dimitri Papadopoulos Orfanos to the list of contributors [#157](https://github.com/bids-standard/bids-specification/pull/157) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
@@ -76,7 +86,7 @@ Changelog
 -   Adding formal decision-making rules [#104](https://github.com/bids-standard/bids-specification/pull/104) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MRG] number of small corrections to the specification [#98](https://github.com/bids-standard/bids-specification/pull/98) ([robertoostenveld](https://github.com/robertoostenveld))
 
-## [v1.1.2](https://bids-specification.readthedocs.io/en/v1.1.2/) (2019-01-10)
+## [v1.1.2](https://github.com/bids-standard/bids-specification/tree/v1.1.2) (2019-01-10)
 
 -   REL: v.1.1.2 [#121](https://github.com/bids-standard/bids-specification/pull/121) ([chrisgorgo](https://github.com/chrisgorgo))
 -   Update 01-contributors.md [#120](https://github.com/bids-standard/bids-specification/pull/120) ([oesteban](https://github.com/oesteban))