From c855abac34e663e2e805e1a9bfef538ba7f2ebd4 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 20 Oct 2024 12:05:04 +0200 Subject: [PATCH] refactor contributing --- CONTRIBUTING.md | 348 ++---------------------------------------------- macros_doc.md | 24 +--- 2 files changed, 18 insertions(+), 354 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index adae5e2cba..f5d9cd972c 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -4,10 +4,15 @@ _We're so excited you're here and want to contribute._ -We hope that these guidelines are designed to make it as easy as possible to get -involved. +We hope that these guidelines are designed to make it as easy as possible to get involved. If you have any questions that aren't discussed below, please let us know -by [opening an issue](#understanding-issues). +by [opening an issue](https://github.com/bids-standard/bids-specification/issues/new). + +If you are not familiar with Git ansd GitHub, +check our [generic contributing guidelines](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html). + +If you want to contribute to the BIDS website, +make sure you also read the instructions below. ## Table of contents @@ -15,114 +20,6 @@ Been here before? Already know what you're looking for in this guide? Jump to the following sections: -- [Joining the BIDS community](#joining-the-community) -- [Contributing through GitHub](#contributing-through-github) -- [Understanding issues](#understanding-issues) -- [Writing in Markdown](#writing-in-markdown) -- [Using macros](#using-macros) -- [Fixing Markdown style errors](#fixing-markdown-style-errors) -- [Using pre-commit hooks](#using-pre-commit-hooks) -- [Adding a figure to the specifications](#adding-a-figure-to-the-specifications) -- [Making a change with a pull request](#making-a-change-with-a-pull-request) -- [Example pull request](#example-pull-request) -- [Commenting on a pull request](#commenting-on-a-pull-request) -- [Accepting suggestion from a review](#accepting-suggestion-from-a-review) -- [Making a change to the BIDS-schema](#making-a-change-to-the-BIDS-schema) -- [How the decision to merge a pull request is made?](#how-is-the-decision-to-merge-a-pull-request-made) -- [How is the changelog generated?](#how-is-the-changelog-generated) -- [Recognizing contributions](#recognizing-contributions) - -## Joining the community - -BIDS - the [Brain Imaging Data Structure](https://bids.neuroimaging.io/) - is a -growing community of neuroimaging enthusiasts, and we want to make our resources -accessible to and engaging for as many researchers as possible. - -How do you know that you're a member of the BIDS community? -You're here! -You know that BIDS exists! -You're officially a member of the community. -It's THAT easy! Welcome! - -Most of our discussions take place here in -[GitHub issues](#understanding-issues). -We also have a -[bids-discussion](https://groups.google.com/forum/#!forum/bids-discussion) -Google Group, although this is largely now an archive of previous conversations. - -Moving forward, we encourage all members to contribute here on -[GitHub](https://github.com/bids-standard/bids-specification) or on the -[NeuroStars](https://neurostars.org/tags/bids) Discourse Forum, under the `bids` -tag. - -To keep on top of new posts, please see this guide for setting your -[topic notifications](https://meta.discourse.org/t/discourse-new-user-guide/96331#heading--topic-notifications). - -As a reminder, we expect that all contributions adhere to our -[Code of Conduct](CODE_OF_CONDUCT.md). - -## Contributing through GitHub - -[Git](https://git-scm.com/) is a really useful tool for version control. -[GitHub](https://github.com/) sits on top of git and supports collaborative and -distributed working. - -We know that it can be daunting to start using git and GitHub if you haven't -worked with them in the past, but the BIDS Specification maintainers are here to -help you figure out any of the jargon or confusing instructions you encounter! - -In order to contribute via GitHub you'll need to set up a free account and sign -in. -Here are some -[instructions](https://help.github.com/articles/signing-up-for-a-new-github-account/) -to help you get going. -Remember that you can ask us any questions you need to along the way. - -## Understanding issues - -Every project on GitHub uses -[issues](https://github.com/bids-standard/bids-specification/issues) slightly -differently. - -The following outlines how BIDS developers think about communicating through -issues. - -**Issues** are individual pieces of work that need to be completed or decisions -that need to be made to move the project forwards. -A general guideline: if you find yourself tempted to write a great big issue -that is difficult to describe as one unit of work, please consider splitting it -into two or more issues. - -Issues are assigned [labels](#issue-labels) which explain how they relate to the -overall project's goals and immediate next steps. - -### Issue labels - -The current list of labels are -[here](https://github.com/bids-standard/bids-specification/labels) and include: - -- [![Help wanted](https://img.shields.io/badge/-help%20wanted-159818.svg)](https://github.com/bids-standard/bids-specification/labels/help%20wanted) - _These issues contain a task that a member of the team has determined we - need additional help with._ - - If you feel that you can contribute to one of these issues, we especially - encourage you to do so! - -- [![Opinions wanted](https://img.shields.io/badge/-opinions%20wanted-84b6eb.svg)](https://github.com/bids-standard/bids-specification/labels/opinions%20wanted) - _These issues hold discussions where we're especially eager for feedback._ - - Ongoing discussions benefit from broad feedback. - This label is used to highlight issues where decisions are being considered, - so please join the conversation! - -- [![Community](https://img.shields.io/badge/-community-%23ddcc5f.svg)](https://github.com/bids-standard/bids-specification/labels/community) - _These issues are related to building and supporting the BIDS community._ - - In addition to the specification itself, we are dedicated to creating a - healthy community. - These issues highlight pieces of work or discussions - around how we can support our members and make it easier to contribute. - ## Writing in Markdown The specification documents follow the @@ -227,7 +124,7 @@ That would look like this: | Manufacturer | Manufacturer of the equipment, for example (`"Siemens"`) | -#### MkDocs admonitions +### MkDocs admonitions It is possible to use [Mkdocs admonitions](https://squidfunk.github.io/mkdocs-material/reference/admonitions/#inline-blocks-inline-end) to highlight certain aspect of the specification. @@ -272,7 +169,7 @@ We have dedicated documentation for this, see the [macros_doc.ms](./macros_doc.m We are using MkDocs to render our specification. Please follow these instructions if you would like to build the specification locally. -#### 1. Download the BIDS specification [repository](https://github.com/bids-standard/bids-specification/tree/master) onto your computer +### 1. Download the BIDS specification [repository](https://github.com/bids-standard/bids-specification/tree/master) onto your computer This can be done by clicking the green button on the right titled "Clone or download" @@ -284,7 +181,7 @@ Or you can use the following `git` command in a terminal: git clone https://github.com/bids-standard/bids-specification.git ``` -#### 2. In the terminal (command line) navigate to your local version of the specification +### 2. In the terminal (command line) navigate to your local version of the specification This location will have the same files you see on our [main specification page](https://github.com/bids-standard/bids-specification). @@ -299,7 +196,7 @@ cd bids-specification Enter all commands below from the command line prompt located at the root of the local version of the specification. -#### 3. Install MkDocs, the Material theme and the required extensions +### 3. Install MkDocs, the Material theme and the required extensions In the following links, you can find more information about @@ -358,7 +255,7 @@ This installs the `bidsschemacode` package in "editable" mode, so that any changes you make to the code will be reflected when you use it, such as when you build the documentation locally. -#### 4. Ready to build! +### 4. Ready to build! Using the terminal (command line) please enter `mkdocs serve`. This will allow you to see a local version of the specification. @@ -440,19 +337,6 @@ Using `remark` to fix some linting errors might introduce some additional change You might have to revert those or use [interactive staging](https://git-scm.com/book/en/v2/Git-Tools-Interactive-Staging) to make sure you only commit the right chunks of code. -## Using pre-commit hooks - -> Git hook scripts are useful for identifying simple issues before submission to code review. - -For more information on Git hooks, see: https://pre-commit.com/. - -Contributors to the bids-specification repository can optionally make use of the `.pre-commit-config.yaml` -configuration file at the root of the repository. -Using Python, simply install `pre-commit` via `pip`, and then run `pre-commit install` from the root -of the bids-specification repository. - -To uninstall the pre-commit hooks, run `pre-commit uninstall`. - ## Adding a figure to the specifications > A figure is worth a 1000 words! @@ -474,6 +358,7 @@ Figures can be inserted in a Markdown like this (see also ```Markdown ![text to show if image does not load](relative_path_to_file "text to show when hovering over image") ``` + ### Recommendations for figures 1. Try to keep the file size of your figure relatively small (smaller than 500 Kb) @@ -491,190 +376,6 @@ future. and how it can be reproduced. Preferably with a link to the file that generated the figure if relevant. -## Making a change with a pull request - -We appreciate all contributions to the BIDS Specification. **THANK YOU** for -helping us build this useful resource. - -#### 1. Comment on an existing issue or open a new issue referencing your addition - -This allows other members of the BIDS Specification team to confirm that you -aren't overlapping with work that's currently underway and that everyone is on -the same page with the goal of the work you're going to carry out. - -#### 2. [Fork](https://help.github.com/articles/fork-a-repo/) [this repository](https://github.com/bids-standard/bids-specification) to your profile - -This is now your own unique copy of the BIDS Specification. -Changes here won't affect anyone else's work, so it's a safe space to explore edits to the -specification! - -Make sure to -[keep your fork up to date](https://help.github.com/articles/syncing-a-fork/) -with the master repository, otherwise you can end up with lots of dreaded -[merge conflicts](https://help.github.com/articles/about-merge-conflicts/). - -#### 3. Make the changes you've discussed - -Try to keep the changes focused. -If you submit a large amount of work in all in one go it will be much more work -for whomever is reviewing your pull request. -Please detail the changes you are attempting to make. - -#### 4. Submit a [pull request](https://help.github.com/articles/about-pull-requests/) - -Please keep the title of your pull request short but informative because it will -appear in the [changelog](src/CHANGES.md) ([see below](#how-is-the-changelog-generated)). - -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) -- `[SCHEMA]` - changes to the BIDS schema and/or related code -- `[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 (also known as a "work in progress" pull request, sometimes abbreviated by `WIP`) -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 -usually 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. - -GitHub has a [nice introduction](https://help.github.com/articles/github-flow/) -to the pull request workflow, but please [get in touch](#get-in-touch) if you -have any questions. - -## Example pull request - -Example-Contribution - -## Commenting on a pull request - -Our primary method of adding to or enhancing BIDS occurs in the form of -[pull requests](https://help.github.com/articles/about-pull-requests/). -BIDS Extension Proposals -([BEPs](https://docs.google.com/document/d/1pWmEEY-1-WuwBPNy5tDAxVJYQ9Een4hZJM06tQZg8X4/)) -are submitted as pull requests, and commenting on pull requests is an important -way of participating in the BIDS community. - -This section outlines how to comment on a pull request. - -### Navigating to open pull requests - -The list of pull requests can be found by clicking on the "Pull requests" tab in -the -[BIDS-Specification repository](https://github.com/bids-standard/bids-specification). - -![BIDS-mainpage](commenting_images/BIDS_GitHub_mainpage.png "BIDS_GitHub_mainpage") - -### Selecting an open pull request - -In this example we will be navigating to our -[BIDS common derivatives pull request](https://github.com/bids-standard/bids-specification/pull/265). - -![BIDS-pr-list](commenting_images/BIDS_pr_list.png "BIDS_pr_list") - -### Pull request description - -Upon opening the pull request we see a detailed description of what this pull -request is seeking to address. -Descriptions are important for reviewers and the community to gain context into -what the pull request is achieving. - -![BIDS-pr](commenting_images/BIDS_pr.png "BIDS_pr") - -### Generally commenting on a pull request - -At the bottom of the pull request page, a comment box is provided for general -comments and questions. - -![BIDS-comment](commenting_images/BIDS_comment.png "BIDS-comment") - -### Specific comments on a pull request - -The proposed changes to the text of the specification can be seen in the "Files -changed" tab. -Proposed additions are displayed on a green background with a `+` -before each added line. -Proposed deletions are displayed on a red background with a `-` before each removed line. -To comment on a specific line, hover over it, and click the blue plus sign (pictured below). -Multiple lines can be selected by clicking and dragging the plus sign. - -![BIDS-specific-comment](commenting_images/BIDS_file_comment.png "BIDS-specific-comment") - -#### Suggesting text - -Comments on lines can contain "suggestions", which allow you to propose specific -wording for consideration. To make a suggestion, click the plus/minus (±) icon -in the comment box (pictured below). - -![BIDS-suggest-box](commenting_images/BIDS_suggest.png "BIDS-suggest") - -Once the button is clicked the highlighted text will be copied into the comment -box and formatted as a -[Markdown code block](https://help.github.com/en/github/writing-on-github/creating-and-highlighting-code-blocks). - -![BIDS-suggest-text](commenting_images/BIDS_suggest_text.png "BIDS-suggest-box") - -The "Preview" tab in the comment box will show your suggestion as it will be -rendered. The "Suggested change" box will highlight the differences between the -original text and your suggestion. - -![BIDS-suggest-change](commenting_images/BIDS_suggest_change.png "BIDS-suggest-change") - -A comment may be submitted on its own by clicking "Add single comment". Several -comments may be grouped by clicking "Start a review". As more comments are -written, accept them with "Add review comment", and submit your review comments -as a batch by clicking the "Finish your review" button. - -## Accepting suggestion from a review - -When others are making [suggestions to your pull request](#suggesting-text), you -have the possibility to accept directly the changes suggested during the review -through the github interface. This can often be faster and more convenient than -make the changes locally and then pushing those changes to update your pull -request. Moreover it gives the opportunity to give credit to the reviewers for -their contribution. - -To do this, you must click on the `Files changed` tab at the top of the page of -a pull request. - -![BIDS_pr_files_changed](commenting_images/BIDS_pr_files_changed.png "BIDS_pr_files_changed") - -From there you can browse the different files changed and the 'diff' for each of -them (what line was changed and what the change consist of). You can also see -comments and directly change suggestions made by reviewers. - -You can add each suggestion one by one or group them together in a batch. - -![BIDS_pr_accept_comment](commenting_images/BIDS_pr_accept_comment.png "BIDS_pr_accept_comment") - -If you decide to batch the suggestions to add several of them at once, you must -scroll back to the top of the 'Files changed' page and the `commit suggestions` -button will let you add all those suggestions as a single commit. - -![BIDS_pr_commit_batch](commenting_images/BIDS_pr_commit_batch.png "BIDS_pr_commit_batch") - -Once those suggestions are committed the commit information should mention the -reviewer as a co-author. - -![BIDS_pr_reviewer_credit](commenting_images/BIDS_pr_reviewer_credit.png "BIDS_pr_reviewer_credit") - ## Making a change to the BIDS-schema Several aspects of the specification are defined in a set of YAML files in the @@ -709,12 +410,6 @@ While the continuous integration run on pull requests by the repository will ren it is crucial to manually review the rendered changes to ensure that the code not only successfully runs, but also that the rendered changes appear as expected. -### 4. Push your changes - -For more information on making general changes with a pull request, please -review -[Making a change with a pull request](#making-a-change-with-a-pull-request). - ## How is the decision to merge a pull request made? The decision-making rules are outlined in @@ -734,21 +429,6 @@ Check the proposed changes and merge the Pull Request at will. To exclude pull requests from showing up in the changelog, they have to be labeled with the "exclude-from-changelog" label. -## 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 contributors in the -[contributors appendix](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html) -of the BIDS specification. - -If you have made any type of contributions to BIDS, -we encourage you to enter or update your information in the -[Contributors wiki page](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors) -according to the instructions listed there. - ## Thank you! You're awesome. diff --git a/macros_doc.md b/macros_doc.md index 6ec9fcf5a2..82c40dfff0 100644 --- a/macros_doc.md +++ b/macros_doc.md @@ -1,3 +1,7 @@ +--- +render_macros: false +--- + # Using MkDocs macros in the BIDS specification We use [mkdocs-macros](https://mkdocs-macros-plugin.readthedocs.io/en/latest/) @@ -9,23 +13,6 @@ in the specification. Below you will find answers to frequently asked questions regarding using macros in the BIDS specification. -- [Using MkDocs macros in the BIDS specification](#using-mkdocs-macros-in-the-bids-specification) - - [What are macros and why use them?](#what-are-macros-and-why-use-them) - - [What kind of input information are required by macros?](#what-kind-of-input-information-are-required-by-macros) - - [What macros are available?](#what-macros-are-available) - - [When should I use a macro?](#when-should-i-use-a-macro) - - [Do I need learn how to program to use those macros?](#do-i-need-learn-how-to-program-to-use-those-macros) - - [Anything else I need to know if I need to insert a new macro call?](#anything-else-i-need-to-know-if-i-need-to-insert-a-new-macro-call) - - [How-To and Examples](#how-to-and-examples) - - [Writing directory content examples](#writing-directory-content-examples) - - [Generating tables](#generating-tables) - - [Modifying a term in the table](#modifying-a-term-in-the-table) - - [Why would you NOT want to modify the content of the yml file directly ?](#why-would-you-not-want-to-modify-the-content-of-the-yml-file-directly-) - - [Adding a new term to the table](#adding-a-new-term-to-the-table) - - [Should I create a macro if I need a new kind of table?](#should-i-create-a-macro-if-i-need-a-new-kind-of-table) - - [Why use macros at all?](#why-use-macros-at-all) - - [Links and references](#links-and-references) - ## What are macros and why use them? A macro is a rule or pattern that specifies how an input should be mapped to @@ -127,9 +114,6 @@ when you get back to the document you just edited) is to leave a comment before the macro to quickly explain what it does and where to find more information about it. - - It could for example look like this: ```markdown