Prepare for package registration

.github/ISSUE_TEMPLATE/bug.yml

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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

.github/ISSUE_TEMPLATE/change.yml

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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
+    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: Link to your project

.github/PULL_REQUEST_TEMPLATE.md

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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.

.github/workflows/CompatHelper.yml

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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()'

.github/workflows/Documentation.yml

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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 }}

.github/workflows/TagBot.yml

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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 }}

.github/workflows/UnitTests.yml

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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 }}

.github/workflows/register.yml

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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 }}

.gitignore

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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

CHANGELOG.md

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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

LICENSE

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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.