From e6a8064b08f1cccfb8cf539b2f9cbe9c128611e8 Mon Sep 17 00:00:00 2001 From: Kevin Bonham Date: Fri, 5 Nov 2021 14:03:10 -0400 Subject: [PATCH] Some other documentation fixes (#97) * update news * some readme improvements * bio->eco * biojulia purge --- CONTRIBUTING.md | 440 +++---------------------------------- NEWS.md | 4 +- README.md | 11 +- docs/src/gettingstarted.md | 8 +- docs/src/humann.md | 8 +- docs/src/metaphlan.md | 8 +- 6 files changed, 58 insertions(+), 421 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a69d759a..faa51e93 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,176 +1,19 @@ -# Contributing to BioJulia +# Contributing to Microbiome.jl and BiobakeryUtils.jl :+1::tada: First off, thanks for taking the time to contribute! :tada::+1: -The following is a set of guidelines for contributing to BioJulia repositories, -which are hosted in the [BioJulia Organization](https://github.com/BioJulia) on -GitHub. +## Etiquette and conduct -These are mostly guidelines, not rules. -Use your best judgment, and feel free to propose changes to this document in a -pull request. - -## Table of contents - -[I don't want to read this whole thing, I just have a question!!!](#i-dont-want-to-read-this-whole-thing-i-just-have-a-question) - -[What should I know about BioJulia before I get started?](#what-should-i-know-about-biojulia-before-i-get-started) - - [BioJulia Package Maintainers](#biojulia-package-maintainers) - - [BioJulia Administrators](#biojulia-administrators) - - [Etiquette and conduct](#etiquette-and-conduct) - - [Package Conventions](#package-conventions) - -[How Can I Contribute?](#how-can-i-contribute) - - [Reporting Bugs](#reporting-bugs) - - [Suggesting an Enhancement](#suggest-an-enhancement) - - [Making Pull Requests](#pull-requests) - - [Become a BioJulia package maintainer](#become-a-biojulia-package-maintainer) - -[Styleguides](#styleguides) - - [Git Commit Messages](#git-commit-messages) - - [Additional julia style suggestions](#additional-julia-style-suggestions) - - [Documentation Styleguide](#documentation-styleguide) - -[Additional notes](#additional-notes) - - [A suggested branching model](#a-suggested-branching-model) - -## I don't want to read this whole thing I just have a question!!! - -We understand you are excited to get involved already! -But please don't file an issue to ask a question. -You'll get faster results by using the resources below. - -We have a Gitter message chat room where the community -chimes in with helpful advice if you have questions. -If you just have a question, or a problem that is not covered by this guide, -then come on over to the Gitter and we'll be happy to help. - -* [Gitter, BioJulia message board](https://gitter.im/BioJulia/Bio.jl) - -## What should I know about BioJulia **BEFORE** I get started? - -### BioJulia Package Maintainers - -In order to provide the best possible experience for new and existing users of -Julia from the life-sciences, a little bit of structure and organization is -necessary. - -Each package is dedicated to introducing a specific data type or algorithm, or -dealing with a specific biological problem or pipeline. - -Whilst there are some "meta-packages" such as Bio.jl, which bundle individual -packages together for convenience of installation and use, most of the BioJulia -software ecosystem is quite decentralized. - -Therefore, it made sense that maintenance of the packages should also be -fairly decentralized, to achieve this, we created the role of a "Package -Maintainer". - -The maintainer(s) for a given package are listed in the packages README.md file. - -The maintainers of a package are responsible for the following aspects of the -package they maintain. - -1. Deciding the branching model used and how branches are protected. -2. Reviewing pull requests, and issues for that package. -3. To tag releases of a package at suitable points in the lifetime of the package. -4. To be considerate and of assistance to new contributors, new community members and new maintainers. -5. To report potential incidents of antisocial to a BioJulia admin member. - -**See [HERE](#additional-notes) for extra -guidance and suggestions on branching models and tagging releases.** - -Package maintainers hold **admin** level access for any package(s) for which they -are listed as maintainer, and so new contributors to BioJulia should -rest assured they will not be 'giving up' any package they transfer to BioJulia, -they shall remain that package's administrator. Package maintainers also have -**push** (but not **admin**) access to all other code packages in the BioJulia -ecosystem. - -This allows for a community spirit where maintainers who are dedicated primarily -to other packages may step in to help other maintainers to resolve a PR or issue. -As such, newer maintainers and researchers contributing a package to the BioJulia -ecosystem can rest assured help will always be at hand from our community. - -However, if you are a maintainer stepping in to help the maintainer(s) dedicated -to another package, please respect them by first offering to step in and help, -before changing anything. Secondly, ask them before doing -advanced and potentially destructive git operations e.g forcing pushes to -branches (especially master), or re-writing history of branches. -Please defer to the judgement of the maintainers dedicated in the README of the -package. - -### BioJulia Administrators - -BioJulia has a select group of members in an Admin team. -This team has administrative access to all repositories in the BioJulia project. - -The admin team is expected to: - -1. Respond and resolve any disputes between any two BioJulia contributors. -2. Act as mentors to all other BioJulia maintainers. -3. Assist maintainers in the upkeep of packages when requested. Especially when - more difficult re-bases and history manipulation are required. -4. Some administrators maintain the BioJulia infrastructure. - This includes being responsible for the accounts and billing of any - platforms used by BioJulia, and the maintenance of any hardware like - servers owned and used by BioJulia. - -### Etiquette and conduct - -BioJulia outlines a [statement of etiquette and conduct](CODE_OF_CONDUCT.md) -that all members and contributors are expected to uphold. Please take the time -to read and understand this statement. - -### Package conventions - -First, be familiar with the official julia documentation on: - -* [Packages](https://docs.julialang.org/en/stable/manual/packages/) -* [Package Development](https://docs.julialang.org/en/stable/manual/packages/#Package-Development-1) -* [Modules](https://docs.julialang.org/en/stable/manual/modules/) - -Package names should be a simple and self explanatory as possible, avoiding -unneeded acronyms. - -Packages introducing some key type or method/algorithm should be named -accordingly. - -For example, the BioJulia package introducing biological sequence types and -functionality to process sequence data is called "BioSequences". -GitHub repository names of BioJulia packages should end in `.jl`, even though -the package name itself does not. -i.e. "BioSequences" is the name of the package, and the name of its GitHub -repository is "BioSequences.jl". - -Considerate and simple naming greatly assists people in finding the kind of -package or functionality they are looking for. - -File names of files containing julia code in packages should end in `.jl`. - -All user facing types and functions (i.e. all types and functions -exported from the module of a package), should be documented. -Documentation regarding specific implementation details that aren't relevant -to users should be in the form of comments. Please *DO* comment liberally for -complex pieces of code! - -We use [Documenter.jl](https://github.com/JuliaDocs/Documenter.jl), -to generate user and developer documentation and host it on the web. -The source markdown files for such manuals is kept in the `docs/src/` -folder of each BioJulia package/repository. - -The code in all BioJulia packages is unit tested. Such tests should be -organized into contexts, and into separate files based on module. - -Files for tests for a module go into an appropriately named folder, within the -`test` folder in the git repo. +Contributors and maintainers for Microbiome.jl and BiobakeryUtils.jl +are expected to abide by the [Julia Community Standards](https://julialang.org/community/standards/) ## How can I contribute? +[(Adapted from the BioJulia's contributing guidelines)](https://github.com/BioJulia/Contributing) + ### Reporting Bugs -Here we show you how to submit a bug report for a BioJulia repository. -If you follow the advice here, BioJulia maintainers and the community will +If you follow the advice here, we will better understand your report :pencil:, be able to reproduce the behaviour :computer: :computer:, and identify related problems :mag_right:. @@ -193,10 +36,6 @@ Please do the following: #### How to create a (good) new bug report: Bugs are tracked as [GitHub issues](https://guides.github.com/features/issues/). -After you've determined [which repository](https://github.com/BioJulia) -your bug is related to, create an issue on that repository and provide the -following information by filling in [template](.github/ISSUE_TEMPLATE.md). -This template will help you to follow the guidance below. When you are creating a bug report, please do the following: @@ -248,39 +87,29 @@ When you are creating a bug report, please do the following: [code block](https://help.github.com/articles/markdown-basics/#multiple-lines) or with a link to a [gist](https://gist.github.com/). -*Note: All of the above guidance is included in the [template](.github/ISSUE_TEMPLATE.md) for your convenience.* ### Suggest an Enhancement -This section explains how to submit an enhancement proposal for a BioJulia -package. This includes completely new features, as well as minor improvements to -existing functionality. +This section explains how to submit an enhancement proposal. +This includes completely new features, as well as minor improvements to existing functionality. Following these suggestions will help maintainers and the community understand your suggestion :pencil: and find related suggestions :mag_right:. #### Before Submitting An Enhancement Proposal -* **Check if there's already [a package](https://github.com/BioJulia) which provides that enhancement.** - -* **Determine which package the enhancement should be suggested in.** - -* **Perform a cursory issue search** to see if the enhancement has already been suggested. - * If it has not, open a new issue as per the guidance below. - * If it has... - * Add a comment to the existing issue instead of opening a new one. - * If it was closed, take the time to understand why this was so (it's ok to - ask! :) ), and consider whether anything has changed that makes the reason - outdated. If you can think of a convincing reason to reconsider the - enhancement, feel free to open a new issue as per the guidance below. +1. **Perform a cursory issue search** to see if the enhancement has already been suggested. +2. If it has not, open a new issue as per the guidance below. +3. If it has... + 1. Add a comment to the existing issue instead of opening a new one. + 2. If it was closed, take the time to understand why this was so (it's ok to + ask! :) ), and consider whether anything has changed that makes the reason + outdated. If you can think of a convincing reason to reconsider the + enhancement, feel free to open a new issue as per the guidance below. #### How to submit a (good) new enhancement proposal Enhancement proposals are tracked as [GitHub issues](https://guides.github.com/features/issues/). -After you've determined which package your enhancement proposals is related to, -create an issue on that repository and provide the following information by -filling in [template](.github/ISSUE_TEMPLATE.md). -This template will help you to follow the guidance below. 1. **Explain the enhancement** - *Use a clear and descriptive title* for the issue to identify the suggestion. @@ -303,7 +132,7 @@ This template will help you to follow the guidance below. 2. **Provide additional context for the enhancement** - - *Explain why this enhancement would be useful* to most BioJulia users and + - *Explain why this enhancement would be useful* to users and isn't something that can or should be implemented as a separate package. - *Do you know of other projects where this enhancement exists?* @@ -314,11 +143,9 @@ This template will help you to follow the guidance below. - Specify the *name and version of the OS* you're using. -*Note: All of the above guidance is included in the [template](.github/ISSUE_TEMPLATE.md) for your convenience.* - ### Making Pull Requests -BioJulia packages (and all julia packages) can be developed locally. +All julia packages can be developed locally. For information on how to do this, see this section of the julia [documentation](https://docs.julialang.org/en/stable/manual/packages/#Package-Development-1). @@ -330,8 +157,9 @@ yourself an account on [Github](https://github.com). The chances are you already have one if you've done coding before and wanted to make any scripts or software from a science project public. -The first step to contributing is to find the -[BioJulia repository](https://github.com/BioJulia) for the package. +The first step to contributing is to find the repository for the package you want to modify +(Microbiome.jl [is here](https://github.com/EcoJulia/Microbiome.jl), +BiobakeryUtils.jl [is here](https://github.com/EcoJulia/BiobakeryUtils.jl)). Hit the 'Fork' button on the repositories page to create a forked copy of the package for your own Github account. This is your blank slate to work on, and will ensure your work and experiments won't hinder other users of the released @@ -339,10 +167,10 @@ and stable package. From there you can clone your fork of the package and work on it on your machine using git. -Here's an example of cloning, assuming you already forked the BioJulia package "BioSequences.jl": +Here's an example of cloning, assuming you already forked `Microbiome.jl`: ```sh -git clone https://github.com//BioSequences.jl.git +git clone https://github.com//Microbiome.jl.git ``` Git will download or "clone" your fork and put it in a folder called @@ -350,8 +178,8 @@ BioSequences.jl it creates in your current directory. It is beyond the scope of this document to describe good git and github use in more specific detail, as the folks at Git and GitHub have already done that wonderfully -on their own sites. If you have additional questions, simply ping a BioJulia -member or the [BioJulia Gitter](https://gitter.im/BioJulia/Bio.jl). +on their own sites. If you have additional questions, +please feel free to start a [discussion on Microbiome.jl](https://github.com/EcoJulia/Microbiome.jl/discussions/new). #### How to make (good) code contributions and new Pull-Requests @@ -377,11 +205,6 @@ member or the [BioJulia Gitter](https://gitter.im/BioJulia/Bio.jl). - Ensure that unit tests have been added which cover your code changes. - - Ensure that you have added an entry to the `[UNRELEASED]` section of the - manually curated `CHANGELOG.md` file for the package. Use previous entries as - an example. Ensure the `CHANGELOG.md` is consistent with the - recommended [changelog style](EXAMPLE_CHANGELOG.md). - - All changes should be compatible with the latest stable version of Julia. @@ -389,8 +212,6 @@ member or the [BioJulia Gitter](https://gitter.im/BioJulia/Bio.jl). 2. **In your pull request** - - **Use the [pull request template](.github/PULL_REQUEST_TEMPLATE.md)** - - *Describe* the changes in the pull request - Provide a *clear, simple, descriptive title*. @@ -413,17 +234,17 @@ member or the [BioJulia Gitter](https://gitter.im/BioJulia/Bio.jl). should provide the results of a simple performance benchmark exercise demonstrating the improvement. Especially if the changes make code less legible. -*Note: All of the above guidance is included in the [template](.github/PULL_REQUEST_TEMPLATE.md) for your convenience.* - #### Reviews and merging You can open a pull request early on and push changes to it until it is ready, or you can do all your editing locally and make a pull request only when it is finished - it is up to you. -When your pull request is ready on Github, mention one of the maintainers of the repo -in a comment e.g. `@Ward9250` and ask them to review it. You can also use Github's -review feature. They will review the code and documentation in the pull request, +When your pull request is ready on Github, +mention one of the maintainers of the repo in a comment e.g. `@kescobo` +and ask them to review it. +You can also use Github's review feature. +They will review the code and documentation in the pull request, and will assess it. Your pull request will be accepted and merged if: @@ -431,77 +252,13 @@ Your pull request will be accepted and merged if: 1. The dedicated package maintainers approve the pull request for merging. 2. The automated build system confirms that all unit tests pass without any issues. -There may be package-specific requirements or guidelines for contributors with -some of BioJulia's packages. Most of the time there will not be, the maintainers -will let you know. - It may also be that the reviewers or package maintainers will want to you to make -changes to your pull request before they will merge it. Take the time to -understand why any such request has been made, and freely discuss it with the -reviewers. Feedback you receive should be constructive and considerate +changes to your pull request before they will merge it. +Take the time to understand why any such request has been made, +and freely discuss it with the reviewers. +Feedback you receive should be constructive and considerate (also see [here](#etiquette-and-conduct)). -### Submitting a package to BioJulia - -If you have written a package, and would like to have it listed under - -and endorsed by - the BioJulia organization, you're agreeing to the following: - -1. Allowing BioJulia to have joint ownership of the package. - This is so that the members can help you review and merge pull requests and - other contributions, and also help you to develop new features. - This policy ensures that you (as the package author and current maintainer) - will have good support in maintaining your package to the highest possible - quality. - -2. Go through a joint review/decision on a suitable package name. - This usually the original package name. However, package authors may be asked - to rename their package to something more official and discoverable (by - search engines and such) if it is contentious or non-standard. - -To submit your package, follow these steps: - -1. Introduce yourself and your package on the BioJulia Gitter channel. -2. At this point maintainers will reach out to mentor and vouch for you and your package. They will: - 1. Discuss with you a suitable name. - 2. Help you ensure the the package is up to standard, and meets the code and contribution guidelines described on this site. - 3. Add you to the BioJulia organisation if you wish to become a BioJulia maintainer. - 4. Transfer ownership of the package. - -### Become a BioJulia package maintainer - -You may ask the current admin or maintainers of a BioJulia package to invite you. - -They will generally be willing to do so if you have done one or -more of the following to [contribute](#how-can-i-contribute) to BioJulia in the past: - -1. You have [submitted a new package](#submitting-a-package-to-biojulia) to BioJulia. -2. [Reported a bug](#reporting-bugs). -3. [Suggested enhancements](#suggesting-enhancements). -4. [Made one or more pull requests](#pull-requests) implementing one or more... - - Fixed bugs. - - Improved performance. - - Added new functionality. - - Increased test coverage. - - Improved documentation. - -None of these requirements are set in stone, but we prefer you to have done one -or more of the above, as it gives good confidence that you are familiar with the -tasks and responsibilities of maintaining a package used by others, and are -willing to do so. -Any other avenue for demonstrating commitment to the community and the -GitHub organisation will also be considered. - -### BioJulia members can sometimes become administrators - -Members of the admin team have often been contributing to BioJulia for a long -time, and may even be founders present at the inception of the project. -In order to become an admin, one does not necessarily have to contribute large -amounts of code to the project. -Rather the decision to on-board a member to an admin position requires a history -of using and contributing to BioJulia, and a positive -interaction and involvement with the community. Any BioJulia member fulfilling -this, may offer to take on this [responsibility](#biojulia-administrators). - ## Styleguides ### Git Commit messages @@ -527,19 +284,6 @@ this, may offer to take on this [responsibility](#biojulia-administrators). ### Additional julia style suggestions -- Source code files should have the following style of header: - - ```julia - # Title - # ===== - # - # Short description. - # - # [Long description (optional)] - # - # This file is a part of BioJulia. License is MIT: - ``` - - Indent with 4 spaces. - For functions that are not a single expression, it is preferred to use an explicit `return`. @@ -615,117 +359,3 @@ name!(node, "somename") # set node name ```julia isvalid(foo) || throw(ArgumentError("$foo is not valid")) ``` - -## Additional Notes - -### A suggested branching model - -If you are a [dedicated maintainer](#biojulia-package-maintainers) on a BioJulia -package, you may be wondering which branching model to choose for development -and maintenance of your code. - -If you are a contributor, knowing the branching model of a package may help -you work more smoothly with the maintainer of the package. - -There are several options available, including git-flow. - -Below is a recommended branching model for your repo, but it is -only a suggestion. What is best for you as the -[dedicated maintainer(s)](#biojulia-package-maintainers), is best for _you_. - -The model below is a brief summary of the ['OneFlow model'](http://endoflineblog.com/oneflow-a-git-branching-model-and-workflow). -We describe it in summary here for convenience, but we recommend you check out -the blog article as a lot more justification and reasoning is presented on _why_ -this model is the way it is. - -#### During development - -1. There is only one main branch - you can call it anything, but usually it's - called `master`. - -2. Use temporary branches for features, releases, and bug-fixes. These temporary - branches are used as a convenience to share code with other developers and as a - backup measure. They are always removed once the changes present on them are - added to master. - -3. Features are integrated onto the master branch primarily in a way which keeps - the history linear and simple. A good compromise to the rebase vs. merge commit - debate for this step is to first do an interactive rebase of the feature branch - on master, and then do a non-fast-forward merge. - Github now does squashed commits when merging a PR and this is fine too. - -_Feature Example:_ - -```sh -git checkout -b feature/my-feature master - -... Make commits to feature/my-feature to finish the feature ... - -git rebase -i master -git checkout master -git merge --no-ff feature/my-feature -git push origin master -git branch -d feature/my-feature -``` - -#### :sparkles: Making new releases - -1. You create a new branch for a new release. It branches off from `master` at the - point that you decided `master` has all the necessary features. This is not - necessarily the tip of the `master` branch. - -2. From then on new work, aimed for the _next_ release, is pushed to `master` as - always, and any necessary changes for the _current_ release are pushed to the - release branch. Once the release is ready, you tag the top of the release branch. - -3. Once the release is ready, tag the top of the release branch with a version - number. Then do a typical merge of the release branch into `master`. - Any changes that were made during the release will now be part of `master`. - Delete the release branch. - -_Release Example:_ - -```sh -git checkout -b release/2.3.0 9efc5d - -... Make commits to release/2.3.0 to finish the release ... - -git tag 2.3.0 -git checkout master -git merge release/2.3.0 -git push --tags origin master -git branch -d release/2.3.0 -git push origin :release/2.3.0 -``` - -7. Do your pushes, and go to GitHub to make your release available. - -#### :bug: Hot-fixes and hot-fix releases - -1. When a hot-fix is needed, create a hot-fix branch, that branches from the - release tag that you want to apply the fix to. - -2. Push the needed fixes to the hot-fix branch. - -3. When the fix is ready, tag the top of the fix branch with a new release, - merge it into master, finally delete the hot-fix branch. - -_Hot-fix example:_ - -```sh -git checkout -b hotfix/2.3.1 2.3.0 - -... Add commits which fix the problem ... - -git tag 2.3.1 -git checkout master -git merge hotfix/2.3.1 -git push --tags origin master -git branch -d hotfix/2.3.1 -``` - -**IMPORTANT:** -There is one special case when finishing a hot-fix branch. -If a release branch has already been cut in preparation for the next release -before the hot-fix was finished, you need to merge the hot-fix branch not to -master, but to that release branch. diff --git a/NEWS.md b/NEWS.md index 4158f422..9b239f68 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,12 +5,12 @@ This version brings a whole host of developments that should make it actually usable. See the [release notes](https://github.com/EcoJulia/BiobakeryUtils.jl/releases/tag/v0.5.0) for details. -Notable features: +See also the JOSS manuscript over at [`Microbiome.jl`](https://github.com/EcoJulia/Microbiome.jl): https://github.com/openjournals/joss-reviews/issues/3876 -- ## Versions 0.2-0.4 Incremental changes, trying to settle on what this package is for. + ## v0.1.0 Liberation from Microbiome.jl This package started off in [Microbiome.jl](https://github.com/BioJulia/Microbiome.jl/). diff --git a/README.md b/README.md index f76ca5b2..c4d9b935 100644 --- a/README.md +++ b/README.md @@ -2,12 +2,16 @@ # BiobakeryUtils.jl +![EcoJulia maintainer: kescobo](https://img.shields.io/badge/EcoJulia%20Maintainer-kescobo-blue.svg) + **Latest Release:** [![Latest Release](https://img.shields.io/github/release/EcoJulia/BiobakeryUtils.jl.svg)](https://github.com/EcoJulia/BiobakeryUtils.jl/releases/latest) + [![](https://img.shields.io/badge/docs-stable-blue.svg)](http://docs.ecojulia.org/BiobakeryUtils.jl/stable/) [![License](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/EcoJulia/BiobakeryUtils.jl/blob/master/LICENSE) -![EcoJulia maintainer: kescobo](https://img.shields.io/badge/EcoJulia%20Maintainer-kescobo-blue.svg) +[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) + **Development Status** @@ -17,11 +21,14 @@ ## Description -BiobakeryUtils.jl is a companion package for [Microbiome.jl](https://github.com/EcoJulia/Microbiome.jl) +`BiobakeryUtils.jl` is a companion package for [`Microbiome.jl`](https://github.com/EcoJulia/Microbiome.jl) for interacting with the [bioBakery](https://github.com/biobakery/biobakery/wiki) family of computational tools authored by the [Huttenhower Lab](http://huttenhower.sph.harvard.edu/) at Harvard. +BiobakeryUtils.jl reexports all functionality from `Microbiome.jl`, +so you never need to do both `using BiobakeryUtils` _and_ `using Microbiome.jl`. + ## Installation Install BiobakeryUtils.jl from the Julia REPL: diff --git a/docs/src/gettingstarted.md b/docs/src/gettingstarted.md index 5a44eaac..408d43a9 100644 --- a/docs/src/gettingstarted.md +++ b/docs/src/gettingstarted.md @@ -11,8 +11,8 @@ Currently, we support [`MetaPhlAn`](https://github.com/biobakery/MetaPhlAn) and Read on to learn how to install the package and use it to begin using it to uncover insights about your microbial community data! -If you run into problems, you can [open an issue](https://github.com/BioJulia/BiobakeryUtils.jl/issues/new/choose) on this repository, -or start a discussion over on [`Microbiome.jl`](https://github.com/BioJulia/Microbiome.jl/discussions/new). +If you run into problems, you can [open an issue](https://github.com/EcoJulia/BiobakeryUtils.jl/issues/new/choose) on this repository, +or start a discussion over on [`Microbiome.jl`](https://github.com/EcoJulia/Microbiome.jl/discussions/new). ## Installing julia @@ -357,5 +357,5 @@ julia> Conda.add("tbb=2020.2", env; channel="conda-forge") ### Still having issues? If your issue isn't addressed here, or you're still having problems, -please [open an issue](https://github.com/BioJulia/BiobakeryUtils.jl/issues/new/choose) -or start a discussion over on [`Microbiome.jl`](https://github.com/BioJulia/Microbiome.jl/discussions/new). +please [open an issue](https://github.com/EcoJulia/BiobakeryUtils.jl/issues/new/choose) +or start a discussion over on [`Microbiome.jl`](https://github.com/EcoJulia/Microbiome.jl/discussions/new). diff --git a/docs/src/humann.md b/docs/src/humann.md index 94a3e414..f52577f6 100644 --- a/docs/src/humann.md +++ b/docs/src/humann.md @@ -12,8 +12,8 @@ end - 🗒️ This tutorial is meant to be run in parallel with / mirror the [official HUMAnN v3 tutorial](https://github.com/biobakery/biobakery/wiki/humann3) - ❓️ If you have questions about HUMAnN itself, please direct them to the [bioBakery help forum](https://forum.biobakery.org/c/Microbial-community-profiling/HUMAnN) -- 🤔 If you have questions about using the MetaPhlAn tools in julia, [please open an issue](https://github.com/BioJulia/BiobakeryUtils.jl/issues/new/choose), - or start a discussion over on [`Microbiome.jl`](https://github.com/BioJulia/Microbiome.jl/discussions/new)! +- 🤔 If you have questions about using the MetaPhlAn tools in julia, [please open an issue](https://github.com/EcoJulia/BiobakeryUtils.jl/issues/new/choose), + or start a discussion over on [`Microbiome.jl`](https://github.com/EcoJulia/Microbiome.jl/discussions/new)! - 📔 For a function / type reference, [jump to the bottom](#Functions-and-Types) ## Installation and setup @@ -220,7 +220,7 @@ julia> first(features(gfs_strat), 5) Here, we can see that the uniref90 "G1UL42" was contributed by _Bacteroides dorei_. -The object returned by `humann_profile` is a `CommunityProfile` type from [`Microbiome.jl`](https://github.com/BioJulia/Microbiome.jl), +The object returned by `humann_profile` is a `CommunityProfile` type from [`Microbiome.jl`](https://github.com/EcoJulia/Microbiome.jl), and has a bunch of useful properties. ### Indexing @@ -287,7 +287,7 @@ julia> features(gfs_strat[["UniRef90_A0A174NIB7", "UniRef90_A6L100"], :]) ``` For more information about indexing and accessing components of the data, -see [the Microbiome.jl docs](https://biojulia.net/Microbiome.jl/latest/profiles/#Indexing-and-selecting-1) +see [the Microbiome.jl docs](https://docs.ecojulia.org/Microbiome.jl/latest/profiles/#Indexing-and-selecting-1) ## Manipulating tables diff --git a/docs/src/metaphlan.md b/docs/src/metaphlan.md index a2bf5fb5..7f7797c1 100644 --- a/docs/src/metaphlan.md +++ b/docs/src/metaphlan.md @@ -12,8 +12,8 @@ end - 🗒️ This tutorial is meant to be run in parallel with / mirror the [official MetaPhlAn v3 tutorial](https://github.com/biobakery/biobakery/wiki/metaphlan3) - ❓️ If you have questions about MetaPhlAn itself, please direct them to the [bioBakery help forum](https://forum.biobakery.org/c/Microbial-community-profiling/MetaPhlAn) -- 🤔 If you have questions about using the MetaPhlAn tools in julia, [please open an issue](https://github.com/BioJulia/BiobakeryUtils.jl/issues/new/choose), - or start a discussion over on [`Microbiome.jl`](https://github.com/BioJulia/Microbiome.jl/discussions/new)! +- 🤔 If you have questions about using the MetaPhlAn tools in julia, [please open an issue](https://github.com/EcoJulia/BiobakeryUtils.jl/issues/new/choose), + or start a discussion over on [`Microbiome.jl`](https://github.com/EcoJulia/Microbiome.jl/discussions/new)! - 📔 For a function / type reference, [jump to the bottom](#Functions-and-Types) ## Installation and setup @@ -327,7 +327,7 @@ julia> metadata(mps3) (sample = "SRS014494", STSite = "Posterior_fornix", filename = "SRS014494-Posterior_fornix_profile.tsv") ``` -[See Microbiome.jl docs](https://biojulia.net/Microbiome.jl/latest/profiles/#working-metadata-1) for more info on metadata and `CommunityProfile`s) +[See Microbiome.jl docs](https://docs.ecojulia.org/Microbiome.jl/latest/profiles/#working-metadata-1) for more info on metadata and `CommunityProfile`s) ## Analyze Results [Official tutorial link](https://github.com/biobakery/biobakery/wiki/metaphlan3#visualize-results) @@ -339,7 +339,7 @@ This means that all of julia's powerful statistics and ML libraries are easy to use with your microbiome data. For more information about indexing and accessing components of the data, -see [the Microbiome.jl docs](https://biojulia.net/Microbiome.jl/latest/profiles/#Indexing-and-selecting-1) +see [the Microbiome.jl docs](https://docs.ecojulia.org/Microbiome.jl/latest/profiles/#Indexing-and-selecting-1) ### Performing PCoA analysis