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Merge pull request #12 from MillironX/registration-prep
Prepare for package registration
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name: Bug | ||
description: Bug report | ||
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body: | ||
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- 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:." | ||
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- type: textarea | ||
validations: | ||
required: true | ||
attributes: | ||
label: Expected behavior | ||
description: Tell us what you expect to happen | ||
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- type: textarea | ||
validations: | ||
required: true | ||
attributes: | ||
label: Current behavior | ||
description: Tell us what happens instead of the expected behavior | ||
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- type: textarea | ||
attributes: | ||
label: Possible solution | ||
description: Suggest a fix/reason for the bug (optional) | ||
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validations: | ||
required: true | ||
attributes: | ||
label: Steps to reproduce | ||
description: You may include copy-pasteable snippets or a list of steps to reproduce the bug | ||
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- 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. | ||
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- type: input | ||
attributes: | ||
label: Package version used | ||
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label: Julia version used | ||
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label: Operating system and version | ||
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- type: input | ||
attributes: | ||
label: Link to your project | ||
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- type: textarea | ||
attributes: | ||
label: Please list installed packages here |
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name: Change | ||
description: Change/improvement suggestion | ||
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body: | ||
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- 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:." | ||
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- type: textarea | ||
validations: | ||
required: true | ||
attributes: | ||
label: Expected behavior | ||
description: Tell us how it should work | ||
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- type: textarea | ||
validations: | ||
required: true | ||
attributes: | ||
label: Current behavior | ||
description: Explain the difference from current behavior | ||
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validations: | ||
required: true | ||
attributes: | ||
label: Possible implementation | ||
description: Suggest ideas how to implement the addition or change | ||
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- 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. | ||
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- type: input | ||
attributes: | ||
label: Link to your project |
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# A clear and descriptive title (No issue numbers please) | ||
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> _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 | ||
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This PR implements the following changes: | ||
_(Please tick any or all of the following that are applicable)_ | ||
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- [ ] :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). | ||
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## :clipboard: Additional detail | ||
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- If you have implemented new features or behaviour | ||
- **Provide a description of the addition** in as many details as possible. | ||
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- **Provide justification of the addition**. | ||
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- **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. | ||
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- If you have changed current behaviour... | ||
- **Describe the behaviour prior to you changes** | ||
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- **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. | ||
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- **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. | ||
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- 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. | ||
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## :ballot_box_with_check: Checklist | ||
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- [ ] :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 | ||
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on: | ||
push: | ||
branches: | ||
- master | ||
- develop | ||
- release/.* | ||
tags: ['*'] | ||
pull_request: | ||
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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 | ||
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on: | ||
- push | ||
- pull_request | ||
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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 | ||
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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 | ||
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# Files generated by invoking Julia with --track-allocation | ||
*.jl.mem | ||
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# 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/ | ||
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# Build artifacts for creating documentation generated by the Documenter package | ||
docs/build/ | ||
docs/site/ | ||
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# 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 | ||
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All notable changes to this project will be documented in this file. | ||
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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). | ||
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## [Unreleased] | ||
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### Added | ||
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- 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` | ||
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[unreleased]: https://github.com/BioJulia/SequenceVariation.jl |
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MIT License | ||
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Copyright (c) 2022 Jakob Nybo Nissen, Thomas A. Christensen II and other contributors. | ||
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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: | ||
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The above copyright notice and this permission notice shall be included in all | ||
copies or substantial portions of the Software. | ||
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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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