Merge pull request #42 from SchlossLab/community

Add community docs

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,131 @@
+# Contributor Covenant Code of Conduct
+
+This document was adapted from the [Tidyverse Code of Conduct](https://tidyverse.tidyverse.org/CODE_OF_CONDUCT.html).
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards
+of acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies
+when an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement
+([Pat Schloss](mailto:pschloss@umich.edu)).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0,
+available at https://www.contributor-covenant.org/version/2/0/
+code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at https://
+www.contributor-covenant.org/translations.

.github/CONTRIBUTING.md

@@ -0,0 +1,35 @@
+# Contributing to mikropml
+
+This document was adapted from the [Tidyverse Contributing guide](https://tidyverse.tidyverse.org/CONTRIBUTING.html).
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation
+directly using the GitHub web interface, as long as the changes are made in the
+_source_ file.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it's needed.
+If you've found a bug, please file an issue that illustrates the bug with a minimal
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+
+### Pull request process
+
+*   Fork the repo and clone onto your computer.
+
+*   Install all [conda and
+    mamba](https://mamba.readthedocs.io/en/latest/installation.html) if you
+    don't already have them.
+
+*   Create a Git branch for your pull request (PR).
+
+*   Make your changes, commit to git, and then create a PR.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+## Code of Conduct
+
+Please note that the mikropml-snakemake-workflow project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

.github/SUPPORT.md

@@ -0,0 +1,27 @@
+# Getting help with mikropml-snakemake-workflow
+
+Thanks for using mikropml-snakemake-workflow!
+Before filing an issue, there are a few places to explore and pieces to put together to make the process as smooth as possible.
+
+## Where to ask?
+
+*   If it's a question: start with [Discussions](https://github.com/SchlossLab/mikropml-snakemake-workflow/discussions), and/or StackOverflow.
+
+*   If it's a bug: you're in the right place, [file an issue](https://github.com/SchlossLab/mikropml-snakemake-workflow/issues/new).
+
+*   If you're not sure: let the community help you figure it out by first asking
+    in Discussions!
+    If your problem _is_ a bug or a feature request, you can easily return here and report it.
+
+Before opening a new issue, be sure to [search issues and pull requests](https://github.com/SchlossLab/mikropml-snakemake-workflow/issues) to make sure the bug hasn't been reported and/or already fixed in the development version.
+By default, the search will be pre-populated with `is:issue is:open`.
+You can [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/)  (e.g. `is:pr`, `is:closed`) as needed. 
+For example, you'd simply remove `is:open` to search _all_ issues in the repo, open or closed.
+
+## What happens next?
+
+To be as efficient as possible, development of our software tends to be very bursty, so you shouldn't worry if you don't get an immediate response.
+Typically we don't look at a repo until a sufficient quantity of issues accumulates, then there's a burst of intense activity as we focus our efforts.
+That makes development more efficient because it avoids expensive context switching between problems, at the cost of taking longer to get back to you.
+This process makes a good reprex particularly important because it might be multiple months between your initial report and when we start working on it.
+If we can't reproduce the bug, we can't fix it!

.github/issue_template.md

@@ -3,12 +3,17 @@ name: Bug report or feature request
 about: Describe a bug you've seen or make a case for a new feature
 ---
 
-Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on <https://stackoverflow.com/> or <https://github.com/SchlossLab/mikropml-snakemake-workflow/discussions/21>.
+Please briefly describe your problem and what output you expect.
+If you have a question, please don't use this form.
+Instead, ask on <https://stackoverflow.com/> or
+<https://github.com/SchlossLab/mikropml-snakemake-workflow/discussions/>.
 
-Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
+Please include a minimal reproducible example (AKA a reprex). If you've never
+heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading
+<https://www.tidyverse.org/help/#reprex>.
+Please include all Snakefiles and scripts used to reproduce the issue.
+If your issue is solely with mikropml and not the accompanying Snakemake
+workflow, open your issue at [the mikropml
+repo](https://github.com/SchlossLab/mikropml) instead.
 
-Brief description of the problem
-
-```r
-# insert reprex here
-```
+Brief description of the problem:

README.md

@@ -52,6 +52,24 @@ your own project.
 Alternatively, you can download this repo and modify the code 
 directly to suit your needs. See instructions [here](/quick-start.md).
 
+## Help & Contributing
+
+If you come across a bug, [open an
+issue](https://github.com/SchlossLab/mikropml-snakemake-workflow/issues)
+and include a minimal reproducible example.
+
+If you have questions, create a new post in
+[Discussions](https://github.com/SchlossLab/mikropml-snakemake-workflow/discussions).
+
+If you’d like to contribute, see our guidelines
+[here](.github/CONTRIBUTING.md).
+
+## Code of Conduct
+
+Please note that the mikropml-snakemake-workflow is released with a
+[Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md).
+By contributing to this project, you agree to abide by its terms.
+
 ## More resources
 
 - [mikropml docs](http://www.schlosslab.org/mikropml/)