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Updated README.md, added contributor's guide, code of conduct, and dev container. (#35)
* added contributors and code of conduct docs. * added dev container. * made new readme.
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‎.devcontainer/Dockerfile

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# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.166.1/containers/ubuntu/.devcontainer/base.Dockerfile
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# [Choice] Ubuntu version: bionic, focal
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ARG VARIANT="focal"
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FROM mcr.microsoft.com/vscode/devcontainers/base:0-${VARIANT}
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# [Optional] Uncomment this section to install additional OS packages.
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RUN export DEBIAN_FRONTEND=noninteractive \
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&& sudo apt-get update \
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&& sudo apt-get -y install golang
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RUN go get -v golang.org/x/tools/gopls
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RUN go get -u github.com/lukehoban/go-outline
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RUN go get -u github.com/uudashr/gopkgs/cmd/gopkgs
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RUN go get github.com/go-delve/delve/cmd/dlv

‎.devcontainer/devcontainer.json

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// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
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// https://github.com/microsoft/vscode-dev-containers/tree/v0.166.1/containers/ubuntu
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{
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"name": "allbase - Ubuntu",
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"build": {
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"dockerfile": "Dockerfile",
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// Update 'VARIANT' to pick an Ubuntu version: focal, bionic
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"args": { "VARIANT": "focal" }
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},
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"terminal.integrated.shell.linux": "/bin/bash"
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": ["golang.go", "ms-vsliveshare.vsliveshare-pack","redhat.vscode-yaml","yzhang.markdown-all-in-one","premparihar.gotestexplorer","github.vscode-pull-request-github","streetsidesoftware.code-spell-checker","eamodio.gitlens"]
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// Use 'forwardPorts' to make a list of ports inside the container available locally.
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// "forwardPorts": [],
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// Use 'postCreateCommand' to run commands after the container is created.
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// "postCreateCommand": "uname -a",
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// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
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// "remoteUser": "vscode"
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}

‎CODE_OF_CONDUCT.md

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

‎CONTRIBUTING.md

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# Introduction
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Yo, what up! if you're reading this then I'm super psyched because that means that you're thinking about contributing to Allbase! Thanks so much for your time and consideration. It's rad people like you that make Allbase such a cool computational synthetic biology tool.
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I wrote this contributor's guide to help newcomers feel welcome. Getting started with a new project can be complicated and I wanted to make it as easy as possible for you to contribute and as easy as possible for me to help.
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Currently any sincere pull request is a good request.
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Allbase is still in pre-release so there are so many way to contribute!
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Here's a list of ideas but feel free to suggest anything I may have forgotten to include.
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* Feature requests - especially cool new algorithms with citations.
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* Devops features. Github action bots, linters, deployment, etc.
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* Unit and integration tests.
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* Writing, editing, and translating tutorials, documentation, or blog posts.
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* Auditing for accessibility.
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* Bug reports.
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* Bug triaging.
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* Community management.
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* Art! Dreams! Your excellence!
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* Code that can be pulled into Allbase itself.
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# Contributor guidelines
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### Excellence, and the contributor's code of conduct
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First up, most importantly we have a contributor's code of conduct. For some reason the internet is a dehumanizing experience and it's easy to forget that aside from the bots we're all humans on this thing. Approach each other with kindness. Please read our [contributor's code of conduct](CODE_OF_CONDUCT.md) and when in doubt just remember our one true rule as once spoken by the ever so wise duo of Bill and Ted.
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`Bill: Be excellent, ... to each other, ...`
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`Ted: and party on, dudes! [sic]`
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![Abraham Licoln saying, "Be Excellent to each other and party on dudes!". [sic]](https://media.giphy.com/media/ef0zYcF7AKu4b0Sns6/giphy-downsized-large.gif)
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### Do-ocracy
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Allbase runs on do-ocracy. Do-ocracy is a simple concept. If you don't like something you don't need permission to fix it, you can just go ahead and fix it! If you actually want to merge your fix, or contribute in someway that benefits everybody, it'd really, really, really help if you got some light consensus from the rest of the Allbase development community but hey, if you really need to do something then you just gotta do it! Just don't expect me to merge it if it doesn't meet our technical criteria or isn't quite right for Allbase.
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### Technical requirements
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Part of what makes Allbase so special is that we have standards. DNA is already spaghetti code on its own and we just don't need to add to that.
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All successfully merged pull requests must meet the following criteria:
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* All current tests must pass.
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* At least one new test must be written to prove that the merged feature works correctly.
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* At least one new [example test](https://blog.golang.org/examples) must be written to demonstrate the merged feature in our docs.
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* Build tests must pass for all currently supported systems and package managers. Linux, Mac OSX, Windows, etc.
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* Code must be clean, readable, and commented. How you do that is up to you!
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Don't worry if you submit a pull request and all the tests break and the code is not readable. We won't merge it just yet and then you can get some feedback about what needs to be changed before we do!
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### Be welcoming
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As one final guideline please be welcoming to newcomers and encourage new contributors from all walks of life. I want Allbase to be for everyone and that includes you and people who don't look, sound, or act like you!
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# Your first contribution
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Unsure where to begin contributing to Allbase? You can start by looking through these beginner and help-wanted issues:
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[Beginner issues](https://github.com/TimothyStiles/allbase/issues?q=is%3Aissue+is%3Aopen+label%3A%22beginner%22+) - issues which should only require a few lines of code, and a test or two.
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[Good first issues](https://github.com/TimothyStiles/allbase/contribute) - issues which are good for first time contributors.
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[Help wanted issues](https://github.com/TimothyStiles/allbase/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22+) - issues which should be a bit more involved than beginner issues.
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[Feature requests](https://github.com/TimothyStiles/allbase/labels/enhancement) - before requesting a new feature search through previous feature requests to see if it's already been requested. If not then feel free to submit a request and tag it with the enhancement tag!
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### Working on your first Pull Request?
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You can learn how from this *free* series, [How to Contribute to an Open Source Project on GitHub](https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github).
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You can also check out [these](http://makeapullrequest.com/) [tutorials](http://www.firsttimersonly.com/).
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At this point, you're ready to make your changes! Feel free to ask for help; everyone is a beginner at first :smile_cat:
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# Getting started
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For something that is bigger than a one or two line fix:
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1. Create your own fork of the code.
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2. Make a branch in your fork
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3. Do the changes in your fork's branch.
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4. Send a pull request.
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## Virtual Environments and Development Containers
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In order to simplify the development experience, and environment setup, the allbase Github repository comes packaged to support *Github CodeSpaces* and [*VSCode Development Containers*](https://code.visualstudio.com/docs/remote/containers#_getting-started). *Github CodeSpaces* will give you ability to spin up a Github hosted instance of Ubuntu that would allow you run, test, develop allbase from the browser. *VSCode Development Containers* in turn will allow your installation of VSCode to spin up a docker instance of Ubuntu on your computer and automatically mount your code onto it so that you continue developing on this docker instance that has all the required development environment setup.
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## Recommended Plugins
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Whether you're a beginner with Go or you're an experienced developer, You should see the suggestions popup automatically when you goto the *Plugins* tab in VSCode. Using these plugins can help accelerate the development experience and also allow you to work more collaboratively with other allbase developers.
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# How to report a bug
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### Security disclosures
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If you find a security vulnerability, do NOT open an issue. I've yet to set up a security email for this so please in the interim DM me on twitter for my email [@timothystiles](https://twitter.com/TimothyStiles).
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In order to determine whether you are dealing with a security issue, ask yourself these two questions:
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* Can I access something that's not mine, or something I shouldn't have access to?
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* Can I disable something for other people?
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If the answer to either of those two questions are "yes", then you're probably dealing with a security issue. Note that even if you answer "no" to both questions, you may still be dealing with a security issue, so if you're unsure, just DM me [@timothystiles](https://twitter.com/TimothyStiles) for my personal email until I can set up a security related email.
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### Non-security related bugs
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For non-security bug reports please [submit it using this template!](https://github.com/TimothyStiles/allbase/issues/new?assignees=&labels=&template=bug_report.md&title=)
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# How to suggest a feature or enhancement
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If you want to suggest a feature it's as easy as filling out this [issue template](https://github.com/TimothyStiles/allbase/issues/new?assignees=&labels=&template=feature_request.md&title=), but before you do please [check to see if it's already been suggested!](https://github.com/TimothyStiles/allbase/labels/enhancement)
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# How add a recommended VSCode Plugin
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Allbase comes with a set of recommended plugins for VSCode. If you have suggestions that will simplify life for the allbase dev community, consider doing a pull-request after modifying `.vscode/extensions.json`.
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# In closing
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Thanks, for reading and I'm super psyched to see what you'll do with Allbase!

‎README.md

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# allbase
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# Allbase
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## All your basepair are belong to us
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## Allbase is a database for engineering organisms
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We're building a modern solution to the biotech data access problem. Too many siloed databases using terrible dataformats that can't crossref eachother. Allbase is still in hot development but as it stands now the plan is to have a single service that can search and cross reference sequences and pathways from genbank, rhea, chembl, and uniprot. All sequences get hashes so they have a unique identifier. Allbase should in the end be able to spit out JSON for every sequence it has and every pathway it can make. Keoni should write down how somewhere but search is going to be dummy fast and easy to use through an API.
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## Specification
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* **Comprehensive:** Allbase is a single service that can search, store, and cross reference sequences and pathways from genbank, rhea, chembl, and uniprot
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* **Modern:** Allbase serves JSON and is written in Go. Allbase parses legacy file formats so you don't have to.
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* **Stable (soon):** Allbase will be well tested and designed to be used in industrial, academic, and hobbyist settings
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## Install
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Allbase is still in hot development and not production ready. We currently only ships a pre-release dev branch for contributors. Join us!
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`git clone https://github.com/TimothyStiles/allbase && cd allbase && go test -v ./...`
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## Community
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* **[Discord](https://discord.gg/Hc8Ncwt):** Chat about Allbase and join us for game nights on our discord server!
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## Contributing
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* **[Code of conduct](CODE_OF_CONDUCT.md):** Please read the full text so you can understand what we're all about and remember to be excellent to each other!
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* **[Contributor's guide](CONTRIBUTING.md):** Please read through it before you start hacking away and pushing contributions to this fine codebase.
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## Sponsor
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* **[Sponsor](https://github.com/sponsors/TimothyStiles):** 🤘 Thanks for your support 🤘
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## License
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* [MIT](LICENSE)
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* Copyright (c) 2022 Timothy Stiles, Keoni Gandall
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<!-- We're building a modern solution to the biotech data access problem. Too many siloed databases using terrible dataformats that can't crossref eachother. Allbase is still in hot development but as it stands now the plan is to have a single service that can search and cross reference sequences and pathways from genbank, rhea, chembl, and uniprot. All sequences get hashes so they have a unique identifier. Allbase should in the end be able to spit out JSON for every sequence it has and every pathway it can make. Keoni should write down how somewhere but search is going to be dummy fast and easy to use through an API. -->
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<!-- ## Specification
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When completed allbase will have:
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* [x] Functions that pull data from Genbank, Rhea, CHEMBL, and Uniprot.
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* [ ] Alignment (will be implemented in Poly).
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* [ ] BWA
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* [ ] minimap2
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* [ ] Insert user provided sequences.
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* [ ] Insert user provided sequences. -->

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