Merge pull request #12 from MillironX/registration-prep

Prepare for package registration
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Thomas A. Christensen II 2022-07-11 18:29:34 +00:00 committed by GitHub
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20 changed files with 535 additions and 242 deletions

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name: Bug
description: Bug report
body:
- type: markdown
attributes:
value: "> _This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you_ :smile:."
- type: textarea
validations:
required: true
attributes:
label: Expected behavior
description: Tell us what you expect to happen
- type: textarea
validations:
required: true
attributes:
label: Current behavior
description: Tell us what happens instead of the expected behavior
- type: textarea
attributes:
label: Possible solution
description: Suggest a fix/reason for the bug (optional)
- type: textarea
validations:
required: true
attributes:
label: Steps to reproduce
description: You may include copy-pasteable snippets or a list of steps to reproduce the bug
- type: textarea
attributes:
label: Context
description: How has this issue affected you? What are you trying to accomplish? Providing context helps us come up with a solution that is most useful in the real world.
- type: input
attributes:
label: Package version used
- type: input
attributes:
label: Julia version used
- type: input
attributes:
label: Operating system and version
- type: input
attributes:
label: Link to your project
- type: textarea
attributes:
label: Please list installed packages here

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name: Change
description: Change/improvement suggestion
body:
- type: markdown
attributes:
value: "> _This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you_ :smile:."
- type: textarea
validations:
required: true
attributes:
label: Expected behavior
description: Tell us how it should work
- type: textarea
validations:
required: true
attributes:
label: Current behavior
description: Explain the difference from current behavior
- type: textarea
validations:
required: true
attributes:
label: Possible implementation
description: Suggest ideas how to implement the addition or change
- type: textarea
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label: Context
description: How has this issue affected you? What are you trying to accomplish? Providing context helps us come up with a solution that is most useful in the real world.
- type: input
attributes:
label: Link to your project

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# A clear and descriptive title (No issue numbers please)
> _This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you_ :smile:. _This template is simply a tool to help everyone remember the BioJulia guidelines, if you feel anything in this template is not relevant, simply delete it._
## Types of changes
This PR implements the following changes:
_(Please tick any or all of the following that are applicable)_
- [ ] :sparkles: New feature (A non-breaking change which adds functionality).
- [ ] :bug: Bug fix (A non-breaking change, which fixes an issue).
- [ ] :boom: Breaking change (fix or feature that would cause existing functionality to change).
## :clipboard: Additional detail
- If you have implemented new features or behaviour
- **Provide a description of the addition** in as many details as possible.
- **Provide justification of the addition**.
- **Provide a runnable example of use of your addition**. This lets reviewers
and others try out the feature before it is merged or makes it's way to release.
- If you have changed current behaviour...
- **Describe the behaviour prior to you changes**
- **Describe the behaviour after your changes** and justify why you have made the changes,
Please describe any breakages you anticipate as a result of these changes.
- **Does your change alter APIs or existing exposed methods/types?**
If so, this may cause dependency issues and breakages, so the maintainer
will need to consider this when versioning the next release.
- If you are implementing changes that are intended to increase performance, you
should provide the results of a simple performance benchmark exercise
demonstrating the improvement. Especially if the changes make code less legible.
## :ballot_box_with_check: Checklist
- [ ] :art: The changes implemented is consistent with the [julia style guide](https://docs.julialang.org/en/v1/manual/style-guide/).
- [ ] :blue_book: I have updated and added relevant docstrings, in a manner consistent with the [documentation styleguide](https://docs.julialang.org/en/v1/manual/documentation/).
- [ ] :blue_book: I have added or updated relevant user and developer manuals/documentation in `docs/src/`.
- [ ] :ok: There are unit tests that cover the code changes I have made.
- [ ] :ok: The unit tests cover my code changes AND they pass.
- [ ] :pencil: I have added an entry to the `[UNRELEASED]` section of the manually curated `CHANGELOG.md` file for this repository.
- [ ] :ok: All changes should be compatible with the latest stable version of Julia.
- [ ] :thought_balloon: I have commented liberally for any complex pieces of internal code.

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name: CompatHelper
on:
schedule:
- cron: 0 0 * * *
workflow_dispatch:
jobs:
CompatHelper:
runs-on: ubuntu-latest
steps:
- name: Pkg.add("CompatHelper")
run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
- name: CompatHelper.main()
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
run: julia -e 'using CompatHelper; CompatHelper.main()'

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name: Documentation
on:
push:
branches:
- master
- develop
- release/.*
tags: ['*']
pull_request:
jobs:
docs:
name: Documentation
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: julia-actions/setup-julia@v1
with:
version: '1'
- run: julia --color=yes --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
- run: julia --color=yes --project=docs docs/make.jl
env:
JULIA_PKG_SERVER: ""
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

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name: TagBot
on:
issue_comment:
types:
- created
workflow_dispatch:
jobs:
TagBot:
if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
runs-on: ubuntu-latest
steps:
- uses: JuliaRegistries/TagBot@v1
with:
token: ${{ secrets.GITHUB_TOKEN }}
ssh: ${{ secrets.DOCUMENTER_KEY }}

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name: Unit Tests
on:
- push
- pull_request
jobs:
test:
name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
julia-version:
- '1.6'
- '1'
- 'nightly'
julia-arch:
- x64
- x86
os:
- ubuntu-latest
- windows-latest
- macOS-latest
exclude:
- os: macOS-latest
julia-arch: x86
steps:
- name: Checkout repository
uses: actions/checkout@v3
- name: Setup Julia
uses: julia-actions/setup-julia@v1
with:
version: ${{ matrix.julia-version }}
arch: ${{ matrix.julia-arch }}
- name: Cache artifacts
uses: actions/cache@v3
env:
cache-name: cache-artifacts
with:
path: ~/.julia/artifacts
key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
restore-keys: |
${{ runner.os }}-test-${{ env.cache-name }}-
${{ runner.os }}-test-
${{ runner.os }}-
- name: Build package
uses: julia-actions/julia-buildpkg@v1
- name: Run tests
uses: julia-actions/julia-runtest@v1
- name: Create CodeCov
uses: julia-actions/julia-processcoverage@v1
- name: Upload CodeCov
uses: codecov/codecov-action@v1
with:
file: lcov.info
flags: unittests
name: codecov-umbrella
fail_ci_if_error: false
token: ${{ secrets.CODECOV_TOKEN }}

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name: Register Package
on:
workflow_dispatch:
inputs:
version:
description: Version to register or component to bump
required: true
jobs:
register:
runs-on: ubuntu-latest
steps:
- uses: julia-actions/RegisterAction@latest
with:
token: ${{ secrets.GITHUB_TOKEN }}

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# Files generated by invoking Julia with --code-coverage
*.jl.cov
*.jl.*.cov
# Files generated by invoking Julia with --track-allocation
*.jl.mem
# System-specific files and directories generated by the BinaryProvider and BinDeps packages
# They contain absolute paths specific to the host computer, and so should not be committed
deps/deps.jl
deps/build.log
deps/downloads/
deps/usr/
deps/src/
# Build artifacts for creating documentation generated by the Documenter package
docs/build/
docs/site/
# File generated by Pkg, the package manager, based on a corresponding Project.toml
# It records a fixed state of all packages used by the project. As such, it should not be
# committed for packages, but should be committed for applications that require a static
# environment.
Manifest.toml

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# Changelog
All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased]
### Added
- Mutation types (`Substitution`, `Deletion`, `Insertion`)
- `Variant` type to store groups of mutations together
- `Variation` type to store and compare individual mutations
- `reconstruct!` function to build mutated sequences from `Variant`s
- `Variant` constructor to automatically detect mutations from a `BioAlignments.PairwiseAlignment`
[unreleased]: https://github.com/BioJulia/SequenceVariation.jl

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MIT License
Copyright (c) 2022 Jakob Nybo Nissen, Thomas A. Christensen II and other contributors.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

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@ -1,6 +1,6 @@
name = "SequenceVariation" name = "SequenceVariation"
uuid = "eef6e190-9969-4f06-a38f-35a110a8fdc8" uuid = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
authors = ["Jakob Nybo Nissen <jakobnybonissen@gmail.com>"] authors = ["Jakob Nybo Nissen <jakobnybonissen@gmail.com>", "Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>"]
version = "0.1.0" version = "0.1.0"
[deps] [deps]
@ -9,6 +9,13 @@ BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59" BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
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[compat]
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julia = "1.6"
[extras] [extras]
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# <img src="docs/src/assets/logo.png" width="30%" align="right" /> SequenceVariation
[![Project Status: WIP Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
[![Latest Release](https://img.shields.io/github/release/BioJulia/SequenceVariation.jl.svg)](https://github.com/BioJulia/SequenceVariation.jl/releases/latest)
[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/SequenceVariation.jl/blob/master/LICENSE)
[![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/SequenceVariation.jl/stable)
[![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/SequenceVariation.jl/dev/)
> This project follows the [semver](https://semver.org) _pro forma_ and uses the [OneFlow branching model](https://www.endoflineblog.com/oneflow-a-git-branching-model-and-workflow).
## Description
SequenceVariation provides a Julia vocabulary for comparing genetic mutations within biological sequences.
## Installation
You can install SequenceVariation from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), and enter the following:
```julia
add https://github.com/SequenceVariation.jl
```
## Testing
SequenceVariation is tested against Julia `1.X` on Linux, OS X, and Windows.
**Latest build status:**
[![Unit tests](https://github.com/BioJulia/SequenceVariation.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/BioJulia/SequenceVariation.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
[![Documentation](https://github.com/BioJulia/SequenceVariation.jl/workflows/Documentation/badge.svg?branch=master)](https://github.com/BioJulia/SequenceVariation.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
[![codecov](https://codecov.io/gh/BioJulia/SequenceVariation.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/SequenceVariation.jl)
## Contributing
We appreciate [contributions](https://github.com/BioJulia/SequenceVariation.jl/graphs/contributors) from users including reporting bugs, fixing issues, improving performance and adding new features.
Take a look at the [contributing files](https://github.com/BioJulia/Contributing) for detailed contributor and maintainer guidelines, and code of conduct.
### Financial contributions
We also welcome financial contributions in full transparency on our [open collective](https://opencollective.com/biojulia).
Anyone can file an expense.
If the expense makes sense for the development the core contributors and the person who filed the expense will be reimbursed.
## Backers & Sponsors
Thank you to all our backers and sponsors!
Love our work and community? [Become a backer](https://opencollective.com/biojulia#backer).
[![backers](https://opencollective.com/biojulia/backers.svg?width=890)](https://opencollective.com/biojulia#backers)
Does your company use BioJulia?
Help keep BioJulia feature rich and healthy by [sponsoring the project](https://opencollective.com/biojulia#sponsor).
Your logo will show up here with a link to your website.
[![](https://opencollective.com/biojulia/sponsor/0/avatar.svg)](https://opencollective.com/biojulia/sponsor/0/website)
[![](https://opencollective.com/biojulia/sponsor/1/avatar.svg)](https://opencollective.com/biojulia/sponsor/1/website)
[![](https://opencollective.com/biojulia/sponsor/2/avatar.svg)](https://opencollective.com/biojulia/sponsor/2/website)
[![](https://opencollective.com/biojulia/sponsor/3/avatar.svg)](https://opencollective.com/biojulia/sponsor/3/website)
[![](https://opencollective.com/biojulia/sponsor/4/avatar.svg)](https://opencollective.com/biojulia/sponsor/4/website)
[![](https://opencollective.com/biojulia/sponsor/5/avatar.svg)](https://opencollective.com/biojulia/sponsor/5/website)
[![](https://opencollective.com/biojulia/sponsor/6/avatar.svg)](https://opencollective.com/biojulia/sponsor/6/website)
[![](https://opencollective.com/biojulia/sponsor/7/avatar.svg)](https://opencollective.com/biojulia/sponsor/7/website)
[![](https://opencollective.com/biojulia/sponsor/8/avatar.svg)](https://opencollective.com/biojulia/sponsor/8/website)
[![](https://opencollective.com/biojulia/sponsor/9/avatar.svg)](https://opencollective.com/biojulia/sponsor/9/website)
## Questions?
If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).

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build/
site/

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[deps]
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
[compat]
Documenter = "0.27"

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using Pkg
using Documenter
using SequenceVariation
makedocs(;
checkdocs = :exports,
linkcheck = true,
sitename = "SequenceVariation.jl",
format = Documenter.HTML(),
modules = [SequenceVariation],
pages = [
"Home" => "index.md",
"API Reference" => "api.md",
],
authors = replace(join(Pkg.TOML.parsefile("Project.toml")["authors"], ", "), r" <.*?>" => "" ) * ", The BioJulia Organisation, and other contributors."
)
deploydocs(
repo = "github.com/BioJulia/SequenceVariation.jl.git",
devbranch = "master",
push_preview = true,
)

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```@meta
CurrentModule = SequenceVariation
DocTestSetup = quote
using SequenceVariation
end
```
# API Reference
```@autodocs
Modules = SequenceVariation
```

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# SequenceVariation.jl
[![Project Status: WIP Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
[![Latest Release](https://img.shields.io/github/release/BioJulia/SequenceVariation.jl.svg)](https://github.com/BioJulia/SequenceVariation.jl/releases/latest)
[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/SequenceVariation.jl/blob/master/LICENSE)
[![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/SequenceVariation.jl/stable)
[![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/SequenceVariation.jl/dev/)
> This project follows the [semver](https://semver.org) _pro forma_ and uses the [OneFlow branching model](https://www.endoflineblog.com/oneflow-a-git-branching-model-and-workflow).
## Description
SequenceVariation provides a Julia vocabulary for comparing genetic mutations within biological sequences.
## Installation
You can install SequenceVariation from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), and enter the following:
```julia
add https://github.com/SequenceVariation.jl
```
## Testing
SequenceVariation is tested against Julia `1.X` on Linux, OS X, and Windows.
**Latest build status:**
[![Unit tests](https://github.com/BioJulia/SequenceVariation.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/BioJulia/SequenceVariation.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
[![Documentation](https://github.com/BioJulia/SequenceVariation.jl/workflows/Documentation/badge.svg?branch=master)](https://github.com/BioJulia/SequenceVariation.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
[![codecov](https://codecov.io/gh/BioJulia/SequenceVariation.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/SequenceVariation.jl)
## Contributing
We appreciate [contributions](https://github.com/BioJulia/SequenceVariation.jl/graphs/contributors) from users including reporting bugs, fixing issues, improving performance and adding new features.
Take a look at the [contributing files](https://github.com/BioJulia/Contributing) for detailed contributor and maintainer guidelines, and code of conduct.
### Financial contributions
We also welcome financial contributions in full transparency on our [open collective](https://opencollective.com/biojulia).
Anyone can file an expense.
If the expense makes sense for the development the core contributors and the person who filed the expense will be reimbursed.
## Backers & Sponsors
Thank you to all our backers and sponsors!
Love our work and community? [Become a backer](https://opencollective.com/biojulia#backer).
[![backers](https://opencollective.com/biojulia/backers.svg?width=890)](https://opencollective.com/biojulia#backers)
Does your company use BioJulia?
Help keep BioJulia feature rich and healthy by [sponsoring the project](https://opencollective.com/biojulia#sponsor).
Your logo will show up here with a link to your website.
[![](https://opencollective.com/biojulia/sponsor/0/avatar.svg)](https://opencollective.com/biojulia/sponsor/0/website)
[![](https://opencollective.com/biojulia/sponsor/1/avatar.svg)](https://opencollective.com/biojulia/sponsor/1/website)
[![](https://opencollective.com/biojulia/sponsor/2/avatar.svg)](https://opencollective.com/biojulia/sponsor/2/website)
[![](https://opencollective.com/biojulia/sponsor/3/avatar.svg)](https://opencollective.com/biojulia/sponsor/3/website)
[![](https://opencollective.com/biojulia/sponsor/4/avatar.svg)](https://opencollective.com/biojulia/sponsor/4/website)
[![](https://opencollective.com/biojulia/sponsor/5/avatar.svg)](https://opencollective.com/biojulia/sponsor/5/website)
[![](https://opencollective.com/biojulia/sponsor/6/avatar.svg)](https://opencollective.com/biojulia/sponsor/6/website)
[![](https://opencollective.com/biojulia/sponsor/7/avatar.svg)](https://opencollective.com/biojulia/sponsor/7/website)
[![](https://opencollective.com/biojulia/sponsor/8/avatar.svg)](https://opencollective.com/biojulia/sponsor/8/website)
[![](https://opencollective.com/biojulia/sponsor/9/avatar.svg)](https://opencollective.com/biojulia/sponsor/9/website)
## Questions?
If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).