Merge remote-tracking branch 'origin/master' into enh-glossary

* origin/master: (404 commits)
  [DOC] Auto-generate changelog entry for PR #460
  Apply suggestions from code review
  label -> index
  drop _part-, introduce _split-
  [DOC] Auto-generate changelog entry for PR #459
  [DOC] Auto-generate changelog entry for PR #465
  fix table
  Update src/99-appendices/06-meg-file-formats.md
  [DOC] Auto-generate changelog entry for PR #441
  inject _part into MEG spec
  update entity table
  FIX: clarify _part
  Apply suggestions from code review
  FIX: clarify participants tsv
  [DOC] Auto-generate changelog entry for PR #457
  Update Release_Protocol.md
  add pdf steps for release protocol
  FIX: remove BESA from list of restricted keywords
  Remove trailing space
  Add reference to PDF on front page of specification
  ...

Conflicts:
	src/02-common-principles.md - had to meld with my previous wording etc.

.circleci/artifact_path

@@ -0,0 +1 @@
+0/site/01-introduction.html

.circleci/config.yml

@@ -1,6 +1,6 @@
 version: 2
 jobs:
-  build:
+  build_docs:
     docker:
       - image: circleci/python:3.6.6
     steps:
@@ -25,6 +25,43 @@ jobs:
           command: pipenv run mkdocs build --clean --strict --verbose
       - store_artifacts:
           path: site
+      - persist_to_workspace:
+          root: .
+          paths: site
+
+  linkchecker:
+    docker:
+      - image: yarikoptic/linkchecker:9.4.0.anchorfix1-1
+    steps:
+      - attach_workspace:
+          at: ~/build
+      - run:
+          command: |
+            if (! git log -1 --pretty=%b | grep REL:) ; then
+            chmod a+rX -R ~
+            linkchecker -t 1 ~/build/site/
+            # check external separately by pointing to all *html so no
+            # failures for local file:/// -- yoh found no better way,
+            linkchecker -t 1 --check-extern --ignore-url 'file:///.*' --ignore-url https://fonts.gstatic.com ~/build/site/*html ~/build/site/*/*.html
+            else
+            echo "Release PR - do nothing"
+            fi
+
+  build_docs_pdf:
+    working_directory: ~/bids-specification/pdf_build_src
+    docker:
+      - image: danteev/texlive:TL2017
+    steps:
+      - checkout:
+          path: ~/bids-specification
+      - run:
+          name: generate pdf version docs
+          command: sh build_pdf.sh
+      - store_artifacts:
+          path: bids-spec.pdf
+      - run:
+          name: remove pdf version from repo
+          command: rm bids-spec.pdf
 
 # Auto changelog collector
   github-changelog-generator:
@@ -40,7 +77,7 @@ jobs:
            working_directory: ~/build
            command: |
              if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
-             github_changelog_generator --user bids-standard --project bids-specification --token ${CHANGE_TOKEN} --output ~/build/CHANGES.md --base ~/build/src/pregh-changes.md --header-label Changelog --no-issues --no-issues-wo-labels --no-filter-by-milestone --no-compare-link --pr-label ""
+             github_changelog_generator --user bids-standard --project bids-specification --token ${CHANGE_TOKEN} --output ~/build/CHANGES.md --base ~/build/src/pregh-changes.md --header-label "# Changelog" --no-issues --no-issues-wo-labels --no-filter-by-milestone --no-compare-link --pr-label ""
              cat ~/build/CHANGES.md
              mv ~/build/CHANGES.md ~/build/src/CHANGES.md
              else
@@ -73,7 +110,7 @@ jobs:
           name: get remark styles
           command: |
            cd ~
-           npm install remark-cli@5.0.0 remark-lint@6.0.2 remark-preset-lint-recommended@3.0.2 remark-preset-lint-markdown-style-guide@2.1.2
+           cat ~/project/npm-requirements.txt | xargs npm install
       - run: # remark the auto generated changes.md
           name: remark on autogenerated CHANGES.md
           command: |
@@ -113,8 +150,8 @@ jobs:
              merge_messsge=$(git log -1 | grep Merge | grep "pull")
              PR_number=$(echo $merge_messsge | cut -d ' ' -f 4)
              git config credential.helper 'cache --timeout=120'
-             git config user.email "franklin.feingold@gmail.com"
-             git config user.name "Changelog-bot"
+             git config user.email "bids.maintenance@gmail.com"
+             git config user.name "bids-maintenance"
              git add ~/build/src/CHANGES.md
              git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
              git push https://${CHANGE_TOKEN}@github.com/bids-standard/bids-specification.git master
@@ -126,7 +163,10 @@ workflows:
   version: 2
   search_build:
     jobs:
-      - build
+      - build_docs
+      - linkchecker:
+          requires:
+            - build_docs
       - github-changelog-generator:
           filters:
                branches:
@@ -143,3 +183,12 @@ workflows:
           filters:
                branches:
                    only: master
+      # Ensure that build_docs_pdf always runs last, so that we can use the CircleCI API link for the "latest" artifact
+      # https://circleci.com/api/v1.1/project/github/bids-standard/bids-specification/latest/artifacts/0/bids-spec.pdf?branch=master
+      - build_docs_pdf:
+          requires:
+               - build_docs
+               - linkchecker
+               - github-changelog-generator
+               - remark
+               - Changelog-bot

.github/ISSUE_TEMPLATE/blank.md

@@ -0,0 +1,7 @@
+---
+name: Blank issue
+about: Create an issue without a template.
+title: ''
+labels: ''
+assignees: ''
+---

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,17 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+---
+
+--- PLEASE READ AND DELETE THE TEXT BELOW BEFORE OPENING THE ISSUE ---
+
+Please ...
+
+- ... describe your problem in detail.
+- ... describe what you expected instead of your problem.
+- ... provide a link to the part of the BIDS specification that is relevant.
+
+--- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE ISSUE ---

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: BIDS NeuroStars forum
+    url: https://neurostars.org/
+    about: Ask (and answer) concrete technical questions or about implementation details around BIDS.
+  - name: BIDS mailing list
+    url: https://groups.google.com/forum/#!forum/bids-discussion
+    about: Use the BIDS mailing list for announcements, and to draw attention to any item related to BIDS

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,21 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+---
+
+--- PLEASE READ AND DELETE THE TEXT BELOW BEFORE OPENING THE ISSUE ---
+
+- Have you checked our contributing guide? It's a helpful resource: https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md
+
+- Is your idea backwards compatible? If not, please add it to the BIDS 2.0 Google Doc instead of opening an issue: https://docs.google.com/document/d/1LEgsMiisGDe1Gv-hBp1EcLmoz7AlKj6VYULUgDD3Zdw/
+
+- Is there already a group working on your idea? Check the BIDS extension proposals: https://bids.neuroimaging.io/get_involved.html#extending-the-bids-specification
+
+- Will your idea potentially require a large effort? Read BEP lead guidelines: https://docs.google.com/document/d/1pWmEEY-1-WuwBPNy5tDAxVJYQ9Een4hZJM06tQZg8X4/
+
+- When you suggest your idea, please try to supply (mock) examples!
+
+--- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE ISSUE ---

.github/pull_request_template.md

@@ -0,0 +1,25 @@
+--- PLEASE READ AND DELETE THE TEXT BELOW BEFORE OPENING THE PULL REQUEST ---
+
+See the [CONTRIBUTING](https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md) guide. Specifically:
+
+- Please keep the title of your pull request (PR) 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 PR:
+  - `[ENH]` - enhancement of the specification that adds a new feature or
+    support for a new data type
+  - `[FIX]` - fix of a typo or language clarification
+  - `[INFRA]` - changes to the infrastructure automating the specification
+    release (for example building HTML docs etc.)
+  - `[MISC]` - everything else including changes to the file listing
+    contributors
+- If you are opening a PR to obtain early feedback, but the changes
+  are not ready to be merged (a.k.a. Work in Progress PR) please
+  use a [draft PR](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
+- After opening the PR, our continuous integration services will automatically check your contribution  for formatting errors and render a preview of the BIDS specification with your changes.
+  To see the checks and preview, scroll down and click on the `show all checks` link.
+  From the list, select the `Details` link of the `ci/circleci: build_docs artifact` check to see the preview of the BIDS specification.
+
+--- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE PULL REQUEST ---

.gitignore

@@ -1 +1,4 @@
-site/
+site/
+.DS_Store
+src/.DS_Store
+src/04-modality-specific-files/.DS_Store

.remarkrc

@@ -4,6 +4,7 @@
     ["lint-no-duplicate-headings", false],
     ["lint-list-item-indent", "tab-size"],
     ["lint-emphasis-marker", "consistent"],
-    ["lint-maximum-line-length", false]
+    ["lint-maximum-line-length", false],
+    ["lint-maximum-heading-length", false]
   ]
 }

.travis.yml

@@ -5,6 +5,6 @@ cache:
   directories:
   - node_modules # NPM packages
 before_script:
-  - npm install remark-cli@5.0.0 remark-lint@6.0.2 remark-preset-lint-recommended@3.0.2 remark-preset-lint-markdown-style-guide@2.1.2
+  - npm install `cat npm-requirements.txt`
 script:
   - remark src/*.md src/*/*.md --frail