Merge pull request #1 from bids-standard/master

Upload changes

.circleci/config.yml

@@ -25,3 +25,121 @@ jobs:
           command: pipenv run mkdocs build --clean --strict --verbose
       - store_artifacts:
           path: site
+
+# Auto changelog collector
+  github-changelog-generator:
+    working_directory: ~/build
+    docker:
+      - image: ferrarimarco/github-changelog-generator:1.14.3
+    steps:
+      - setup_remote_docker:
+           version: 17.11.0-ce
+      - checkout
+      - run:
+           name: Build changelog
+           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 ""
+             cat ~/build/CHANGES.md
+             mv ~/build/CHANGES.md ~/build/src/CHANGES.md
+             else
+             echo "Commit or Release, do nothing"
+             fi
+      - persist_to_workspace:
+             root: .
+             paths: src
+
+# Clear remark test
+  remark:
+    working_directory: ~
+    docker:
+      - image: node:latest
+    steps:
+      - checkout
+      - attach_workspace:
+          at: ~/build
+      - run:
+          name: update-npm
+          command: |
+           cd ~
+           npm install npm@latest
+      - run:
+          name: get remark
+          command: |
+           cd ~
+           npm install remark remark-cli
+      - run:
+          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
+      - run: # remark the auto generated changes.md
+          name: remark on autogenerated CHANGES.md
+          command: |
+             cd ~/project
+             if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
+             mkdir ~/project/src/tmp
+             cat ~/build/src/CHANGES.md
+             cp ~/build/src/CHANGES.md ~/project/src/CHANGES.md
+             ~/node_modules/.bin/remark ~/project/src/CHANGES.md -o ~/project/src/tmp/CHANGES.md
+             ~/node_modules/.bin/remark ~/project/src/tmp/CHANGES.md --frail
+             else
+             echo "Commit or Release, do nothing"
+             mkdir ~/project/src/tmp
+             touch ~/project/src/tmp/empty.txt
+             fi
+      - persist_to_workspace:
+             root: ~/project/src
+             paths: tmp
+
+# Push built changelog to repo
+  Changelog-bot:
+    working_directory: ~/build
+    docker:
+      - image: circleci/openjdk:8-jdk
+    steps:
+      - setup_remote_docker:
+           version: 17.11.0-ce
+      - checkout
+      - attach_workspace:
+            at: ~/build
+      - deploy:
+           name: Changelog deployment
+           working_directory: ~/build
+           command: |
+             if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
+             mv ~/build/tmp/CHANGES.md ~/build/src/CHANGES.md
+             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 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
+             else
+             echo "Commit or Release, do nothing"
+             fi
+
+workflows:
+  version: 2
+  search_build:
+    jobs:
+      - build
+      - github-changelog-generator:
+          filters:
+               branches:
+                   only: master
+      - remark:
+          requires:
+               - github-changelog-generator
+          filters:
+               branches:
+                   only: master
+      - Changelog-bot:
+          requires:
+               - remark
+          filters:
+               branches:
+                   only: master

.remarkrc

@@ -1,6 +1,9 @@
 {
   "plugins": [
     "preset-lint-markdown-style-guide",
-    ["lint-no-duplicate-headings", false]
+    ["lint-no-duplicate-headings", false],
+    ["lint-list-item-indent", "tab-size"],
+    ["lint-emphasis-marker", "consistent"],
+    ["lint-maximum-line-length", false]
   ]
 }

CODEOWNERS

@@ -0,0 +1,16 @@
+# This files DOES NOT list people responsible for maintenance of different parts of
+# the specification. It merely serves the purpose of notifying interested
+# contributors when a new Pull Request that proposes changes to a particular file
+# is submitted. If you would like to subscribe to such notifications (in a form of a
+# 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/99-appendices/06-meg-file-formats.md @monkeyman192

CONTRIBUTING.md

@@ -44,9 +44,9 @@ The specification documents follow the [Markdown Style Guide](http://www.cirosan
 You
 can validate your changes against the guide using [remark](https://github.com/remarkjs/remark-lint) which works as a
 [standalone command line tool](https://github.com/remarkjs/remark/tree/master/packages/remark-cli) as well as [a plugin for various text editors](https://github.com/remarkjs/remark-lint#editor-integrations). Remark preserves consistent markdown styling across the contributions. Please ensure before submitting a contribution that you do not have any linter errors in your text editor.
-You can also use [prettier](https://github.com/prettier/prettier) to automatically correct some of the style issuse that might be found in the proposed changes.
+You can also use [prettier](https://github.com/prettier/prettier) to automatically correct some of the style issues that might be found in the proposed changes.
 
-We have deployed a continous integrator ([circle CI](https://circleci.com/)) to further allow for integrating changes continously. The CI is testing that the changes are inline with our standard styling.
+We have deployed a continuous integrator ([circle CI](https://circleci.com/)) to further allow for integrating changes continuously. The CI is testing that the changes are inline with our standard styling.
 
 GitHub has a helpful page on [getting started with writing and formatting on GitHub](https://help.github.com/articles/getting-started-with-writing-and-formatting-on-github).
 
@@ -95,9 +95,25 @@ Try to keep the changes focused. If you submit a large amount of work in all in
 
 #### 4. Submit a [pull request](https://help.github.com/articles/about-pull-requests/)
 
+Please keep the title of your pull request short but informative - it will 
+appear in the [changelog](src/CHANGES.md).
+
+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
+  - `[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 pull request to obtain early feedback, but the changes 
+are not ready to be merged (a.k.a. Work in Progress pull request) please 
+use a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
+
 A member of the BIDS Specification team will review your changes to confirm that they can be merged into the main codebase.
 
-A [review](https://help.github.com/articles/about-pull-request-reviews/) will probably consist of a few questions to help clarify the work you've done. Keep an eye on your github notifications and be prepared to join in that conversation.
+A [review](https://help.github.com/articles/about-pull-request-reviews/) will probably consist of a few questions to help clarify the work you've done. Keep an eye on your GitHub notifications and be prepared to join in that conversation.
 
 You can update your [fork](https://help.github.com/articles/about-forks/) of the BIDS Specification and the pull request will automatically update with those commits. You don't need to submit a new pull request when you make a change in response to a review.
 
@@ -110,6 +126,10 @@ GitHub has a [nice introduction](https://help.github.com/articles/github-flow/)
 
 <br>
 
+## How the decision to merge a pull request is made?
+
+The decision-making rules are outlined in [DECISION-MAKING.md](DECISION-MAKING.md).
+
 ## Recognizing contributions
 
 BIDS follows the [all-contributors](https://github.com/kentcdodds/all-contributors) 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).

DECISION-MAKING.md

@@ -0,0 +1,106 @@
+# Decision-making rules
+
+## Introduction
+
+The Brain Imaging Data Structure (BIDS) community set out the following
+decision-making rules with the intention to:
+
+- Strive for consensus.
+- Promote open discussions.
+- Minimize the administrative burden.
+- Provide a path for when consensus cannot be made.
+- Grow the community.
+- Maximize the [bus factor](https://en.wikipedia.org/wiki/Bus_factor) of the
+  project.
+
+The rules outlined below are inspired by the [lazy consensus system used in the Apache Foundation](https://www.apache.org/foundation/voting.html)
+and heavily depends on [GitHub Pull Request Review system](https://help.github.com/articles/about-pull-requests/).
+
+## Definitions
+
+**Repository** - [https://github.com/bids-standard/bids-specification](https://github.com/bids-standard/bids-specification)
+
+**Contributor** - a person listed in the Appendix I: Contributors. The
+community decides on the content of this file using the same process as any
+other change to the Repository (see below) allowing the meaning of "Contributor"
+to evolve independently of the Decision-making rules.
+
+**Maintainer** - a Contributor responsible for the long term health of the
+project and the community. Maintainers have additional rights (see Rules)
+helping them to resolve conflicts and increase the pace of the development
+when necessary. Current Maintainers:
+
+| Name                                                            | Time commitment |
+|-----------------------------------------------------------------|-----------------|
+| Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff)) | 5h/week         |
+
+## Rules
+
+1. Every modification of the specification (including a correction of a typo,
+   adding a new Contributor, an extension adding support for a new data type, or
+   others) or proposal to release a new version needs to be done via a Pull
+   Request (PR) to the Repository.
+1. Anyone can open a PR (this action is not limited to Contributors).
+1. PRs adding new Contributors must also add their GitHub names to the
+   [CODEOWNERS](CODEOWNERS) file.
+1. A PR is eligible to be merged if and only if these conditions are met:
+   1. The last commit is at least 5 working days old to allow the community to
+      evaluate it.
+   1. The PR features at least two [Reviews that Approve](https://help.github.com/articles/about-pull-request-reviews/#about-pull-request-reviews)
+      the PR from Contributors of which neither is the author of the PR. The reviews
+      need to be made after the last commit in the PR (equivalent to
+      [Stale review dismissal](https://help.github.com/articles/enabling-required-reviews-for-pull-requests/)
+      option on GitHub).
+   1. Does not feature any [Reviews that Request changes](https://help.github.com/articles/about-required-reviews-for-pull-requests/).
+   1. Does not feature "WIP" in the title (Work in Progress).
+   1. Passes all automated tests.
+   1. Is not proposing a new release or has been approved by at least one
+      Maintainer (i.e., PRs proposing new releases need to be approved by at
+      least one Maintainer).
+1. A Maintainer can merge any PR - even if it's not eligible to merge according
+   to Rule 4.
+1. Any Contributor can Review a PR and Request changes. If a Contributor
+   Request changes they need to provide an explanation what changes
+   should be added and justification of their importance. Reviews requesting
+   changes can also be used to request more time to review a PR.
+1. A Contributor that Requested changes can Dismiss their own review or Approve
+   changes added by the Contributor who opened the PR.
+1. If the author of a PR and Contributor who provided Review that Requests
+   changes cannot find a solution that would lead to the Contributor dismissing
+   their review or accepting the changes the Review can be Dismissed with a
+   vote or by a Maintainer. Rules governing voting:
+   1. A Vote can be triggered by any Contributor, but only after 5 working days
+      from the time a Review Requesting Changes has been raised and in case a
+      Vote has been triggered previously no sooner than 15 working days since
+      its conclusion.
+   1. Only Contributors can vote, each contributor gets one vote.
+   1. A Vote ends after 5 working days or when all Contributors have voted
+      (whichever comes first).
+   1. A Vote freezes the PR - no new commits or Reviews Requesting changes can
+      be added to it while a vote is ongoing. If a commit is accidentally made
+      during that period it should be reverted.
+   1. The quorum for a Vote is 30% of all Contributors.
+   1. The outcome of the vote is decided based on a simple majority.
+
+## Comments
+
+1. Researchers preparing academic manuscripts describing work that has been
+   merged into this repository are strongly encouraged to invite all
+   Maintainers as co-authors as a form of appreciation for their work.
+1. There are no restrictions on how the content of the PR is prepared. For
+   example it is perfectly fine for a PR to consist of content developed by a
+   group of experts over an extended period of time via in person meetings and
+   online collaborations using a Google Document.
+1. To facilitate triage of incoming PR you can subscribe to
+   notifications for new PRs proposing changes to specific files. To do this
+   add your GitHub name next to the file you want to subscribe to in the
+   [CODEOWNERS](CODEOWNERS). This way you will be ask to review each relevant
+   PR. Please mind that lack of your review will not prevent the PR from being
+   merged so if you think the PR needs your attention, please review it
+   promptly or request more time via Request changes.
+1. Releases are triggered the same way as any other change - via a PR.
+1. PRs MUST be merged using the "Create a merge commit" option in GitHub (i.e.,
+   the "merge pull request" option). This is necessary for our automatic
+   changelog generator to do its work reliably. See the [GitHub help page](https://help.github.com/en/articles/about-merge-methods-on-github)
+   for information on merge methods. See the changelog generator implementation
+   in our [circleci configuration file](./.circleci/config.yml).

Pipfile

@@ -5,7 +5,7 @@ name = "pypi"
 
 [packages]
 mkdocs = "==1.0.4"
-mkdocs-material = "==3.0.4"
+mkdocs-material = "==4.1.2"
 
 [dev-packages]